Rationale
The process of science may be described as noting what you see and using it to create an explanation
of what you don't see. It is of the utmost importance to make a clear distinction between
the observation and the explanation. It is important that you internalize the concept, make it an integral
part of how you think about science, and to do this, nothing beats practice.
In this exercise, you'll take a gene from bacteriophage T4 whose function has been described and look for
an empirical justification for that description. That justification will be at least one specific experiment
from a research article. You'll add a brief summary of the experiment to the record of your gene. In doing
so, you'll provide a service to the community of phage researchers.
Why bacteriophage? Why T4?
(This section is primarily for people who did not pass through Phage Lab)
The history of molecular biology has threaded through it the study of bacteriophages,
i.e. viruses that infect bacteria. This makes a good deal of sense. Bacteriophages are amongst the
smallest of biological entities with a reproductive cycle measured in minutes. Their simplicity
and huge numbers made possible many of the articles we will read. You can read more along these lines
by going through Why study bacteriophage?
E. coli bacteriophage T4 is perhaps the best studied of all bacteriophages
(with the possible exception of bacteriophage lambda). Its genome contains genes for a large number of
proteins whose functions have been described.
How to become a phage annotator
Phantome/BioBIKE
provides a means through which the bacteriophage research community can access a
knowledge-base concerning bacteriophages and bacteria and can contribute knowledge.
As with Wikipedia, anyone can contribute to the resource, but Phantome/BioBIKE insists
that contributions not be anonymous. Every assertion should contain a justification for it
and a means of contacting the person making the assertion.
It is therefore necessary to provide contact information before annotating a gene.
To do this:
- Open up Firefox. Unfortunately, no other browser will work. If you don't already have Firefox,
go to the Firefox website to download the latest version.
- Within Firefox, go to the BioBIKE portal
- Click the public site for PhAnToMe/BioBIKE
- Enter either your email address or some user name that will be memorable to you and that you'll use henceforth
- Click New Login
- Fill in the four boxes (your affiliation will probably be "Virginia Commonwealth University")
- Click Register
After all this, you'll be brought into PhAnToMe/BioBIKE.
Mechanics of annotating a gene
- In a separate browser window, go to the BioBIKE portal
- Click Guided tours of BioBIKE
- Click Integration of Experimental Evidence
- Go through the guided tour. The first two-thirds presents a scientific context. The last third
gives an example of how you'd begin to annotate a gene.
- Try it yourself, using the INFORMATION-ABOUT-GENE/S function, obtainable from the
GENES-PROTEINS button, to go to the annotation window for bacteriophage T4 gene T4p113.
Recreate what you saw in the tour (but don't try to annotate this gene!)
- When the time comes to annotate a gene yourself, you will click the entry box for Main annotation
and enter four things:
- (Maybe) In the yellow box, a short description of the gene function. In most cases, the given
description will be fine and you won't need to do anything.
- In the Evidence box, a brief description of the experiment justifying the description,
referring to the research article that contained the experiment.
- In the Evidence link box, provide a link to the article that contained the evidence.
- For Evidence Inferred From, click the Lab experiment radio button.
- When satisfied, click Save
How to choose a gene
- You'll want to choose a gene for which a function is known. Avoid genes annotated as "hypothetical" or "phage protein".
There are 283 T4 genes, 177 of which have meaningful annotations, so there are plenty to choose from.
- Choose a gene that does not already have a good annotation of function. Very few T4 genes have good
annotations, but one that does and may serve as an example is T4 gene T4p006.
- You can get a list of genes of T4 and their current annotations by bringing down the DESCRIPTION-OF function
from the GENES-PROTEINS button, clicking the entity box to open it, bringing down the GENES-OF function (from the GENOMES menu), opening its entity box, and typing ent-T4 (the nickname of Enterobacteria Phage T4). Then close the box (click Enter), and execute the function (e.g. double-clicking the name of the function).
- Alternatively, you can look for a review article on the genome of T4 that can provide descriptions for all of
its genes.
- Feel free to annotate a gene that someone else has already annotated, if you think there's something wrong with
the original annotation. But don't destroy an existing annotation that you can find no fault with.
How to find evidence to justify the annotation
Well, here's a prime opportunity to put into action the lessons learned from Problem Set 1!
You might try a key word search, or an easier route is to use a review article on the T4 genome to point you
to useful references. Whatever you do, in the end, you're going to want to have a research article that describes
an experiment that justifies the given functional annotation.