Monthly Archives: January 2015

WP PubMed Reflist

I committed a couple of updates to my WordPress plugin for getting reference lists from PubMed. The new version allows customization of the display. I preloaded some templates that approximate a few popular formats

NIH format

  1. Giglio, M, Tauber, R, Nadendla, S, Munro, J, Olley, D, Ball, S et al.. ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res. 2018; :. doi: 10.1093/nar/gky1036. PubMed PMID:30407590 .
  2. Chibucos, MC, Siegele, DA, Hu, JC, Giglio, M. The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. Methods Mol. Biol. 2017;1446 :245-259. doi: 10.1007/978-1-4939-3743-1_18. PubMed PMID:27812948 .
  3. Gaudet, P, Škunca, N, Hu, JC, Dessimoz, C. Primer on the Gene Ontology. Methods Mol. Biol. 2017;1446 :25-37. doi: 10.1007/978-1-4939-3743-1_3. PubMed PMID:27812933 .
  4. Nehring, RB, Gu, F, Lin, HY, Gibson, JL, Blythe, MJ, Wilson, R et al.. An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli. Nucleic Acids Res. 2016;44 (5):e41. doi: 10.1093/nar/gkv1131. PubMed PMID:26578563 PubMed Central PMC4797258.
  5. Chibucos, MC, Zweifel, AE, Herrera, JC, Meza, W, Eslamfam, S, Uetz, P et al.. An ontology for microbial phenotypes. BMC Microbiol. 2014;14 :294. doi: 10.1186/s12866-014-0294-3. PubMed PMID:25433798 PubMed Central PMC4287307.
Search PubMed

ASM format

  1. Giglio, M, Tauber, R, Nadendla, S, Munro, J, Olley, D, Ball, S, Mitraka, E, Schriml, LM, Gaudet, P, Hobbs, ET, Erill, I, Siegele, DA, Hu, JC, Mungall, C, Chibucos, MC. 2018. ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res. :.
  2. Chibucos, MC, Siegele, DA, Hu, JC, Giglio, M. 2017. The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. Methods Mol. Biol. 1446:245-259.
  3. Gaudet, P, Škunca, N, Hu, JC, Dessimoz, C. 2017. Primer on the Gene Ontology. Methods Mol. Biol. 1446:25-37.
  4. Nehring, RB, Gu, F, Lin, HY, Gibson, JL, Blythe, MJ, Wilson, R, Bravo Núñez, MA, Hastings, PJ, Louis, EJ, Frisch, RL, Hu, JC, Rosenberg, SM. 2016. An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli. Nucleic Acids Res. 44:e41.
  5. Chibucos, MC, Zweifel, AE, Herrera, JC, Meza, W, Eslamfam, S, Uetz, P, Siegele, DA, Hu, JC, Giglio, MG. 2014. An ontology for microbial phenotypes. BMC Microbiol. 14:294.
Search PubMed

PNAS format

  1. Giglio, M et al.(2018)ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res. :.
  2. Chibucos, MC, Siegele, DA, Hu, JC, Giglio, M(2017)The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. Methods Mol. Biol. 1446 :245-259.
  3. Gaudet, P, Škunca, N, Hu, JC, Dessimoz, C(2017)Primer on the Gene Ontology. Methods Mol. Biol. 1446 :25-37.
  4. Nehring, RB et al.(2016)An ultra-dense library resource for rapid deconvolution of mutations that cause phenotypes in Escherichia coli. Nucleic Acids Res. 44 (5):e41.
  5. Chibucos, MC et al.(2014)An ontology for microbial phenotypes. BMC Microbiol. 14 :294.
Search PubMed

Notes

The formatting options in 0.7+ allow handling of long author lists to give et al. were there are too many authors.

Because I do WordPress development only sporadically, I made some errors in the 0.7 release. I do my testing on my Mac, where unfortunately I set my laptop up to have case-insensitive filenames, and had a uppercase vs lowercase filename error in the subversion commit for 0.7. When fixing the filenames on a Mac, you can’t just use svn mv filename fileName. You get an uninformative error. You have to do it in two steps doing something like this:

  • svn mv filename filename.tmp
  • svn mv filename.tmp fileName