Author Archives: jimhu

Not so new big news

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We’re updating how we provide the latest news about the OMP project to feed items from our blog to the homepage of the OMP wiki and to automatically tweet to @micropheno. We have two big news items that we failed to post earlier

  • OMP got funded by NIH!
  • ECO now has its own funding from NSF (we will continue to provide our wiki-based ECO browser)

OMP paper in BMC Genomics

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Our first publication describing how we’ve designed OMP was published in BMC Genomics

  1. 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 Microbiol14,294.
Search PubMed

Letters of support for OMP

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Dear Colleagues,

We are writing to request letters of support for the renewal of our grant: “An ontology for bacterial phenotypes”. The co-PIs for the project are Jim Hu and Debby Siegele at Texas A&M and Michelle Gwinn-Giglio and Marcus Chibucos from the Institute for Genome Sciences at the University of Maryland School of Medicine.

The long-term goal of the Ontology for Microbial Phenotypes (OMP) project is to create a common system for capturing phenotype information for all microbes in a way that will enhance analysis of microbial genetics and comparative genetics across different microbial systems. In our first funding period, we designed a data model for annotation of phenotypes and began development of the ontology.

The most basic phenotype annotation in OMP consists of a genotype whose phenotype is associated with an OMP term to capture the phenotype, a reference, an Evidence Code Ontology (ECO) term to assert the way the phenotype was observed, and an optional relationship to another annotation to capture how phenotypes are different relative to a control. We created the OMP wiki (http://microbialphenotypes.org) as a website to search and browse OMP and ECO, and as a place to capture literature-based phenotype annotations. We have begun collecting phenotype observations for E. coli K-12 using the prototype annotation system.

The aims for our renewal are:

  • to continue development of the Ontology for Microbial Phenotypes
  • to continue coordination of of development Evidence Code Ontology terms needed for annotation of phenotypes
  • the development of a database of microbial genotypes and alleles, which is needed to support the long-term value of phenotype annotation
  • to continue development of online resources and curation tools for phenotype annotation
  • further phenotype annotation with the focus of ensuring the annotation system can express phenotype data from microbial model genetic systems, starting with E. coli lab strains and then moving on to E. coli clinical strains and finally other species, both prokaryotic and eukaryotic

One of our goals is to build OMP from the start as a system with a strong community input component for both the ontology development and the annotation infrastructure, so your letter will not only help our chances of renewed funding but will provide us with feedback from potential users. We think your letter would be most effective if it could address the following: What specific questions is your lab interested in and what are your sources of funding? How will the development of a microbial phenotype ontology help your group in their research? If you can provide specific examples, that will really help. Can we contact you with questions where your area of expertise can add to the success of the project?

We hope you will be able to send a letter expressing your support for continued funding of OMP by June 25. Please send the letter as a pdf on letterhead to siegele@bio.tamu.edu. A copy of the letter you wrote for the previous submission is attached.

Many thanks,

Marcus Chibucos
Michelle Gwinn Giglio
Jim Hu
Debby Siegele