About the HOPS Resource
Hypotheses and Open Problems revealed by Subsystems)
Sequencing and analysis of hundreds, soon to be thousands, of genomes
reveals multiple gaps in our knowledge of basic biochemical and
cellular processes. Accurate mapping of the revealed open problems
within a framework of specific subsystems and groups of organisms sets
the stage for generating hypotheses amenable to experimental
validation. In a growing number of cases, predictions of novel genes
and pathways delivered by comparative genomics techniques (eg analysis
of gene clustering on prokaryotic chromosomes) get successfully
verified. Based on this vision, the scope of this web-site is to build
and maintain the public repository of:
- Well-defined open problems (knowledge gaps) revealed by comparative genome analysis of various subsystems. Major types of such problems (eg "missing genes" or "functionally coupled hypotheticals" etc) are listed Help on How to Pick problem Types..
- Hypotheses, testable predictions pertaining to these problems.
- Records of experimental follow-up and comments on any of the suggested hypotheses (in a range from "intend to test" to "proven right/wrong").
It is important to emphasize that we aim to restrict the breadth of
open problems to those that, are:
-
in specific functional context. For example, in general, we
avoid recording questions like: "what is the function of this
hypothetical protein?". On the other hand, "missing gene" questions of
a form: "what gene encodes this enzyme in otherwise complete
pathway?", are highly valued.
- within the realm of genome comparative analysis. We realize
that many interesting problems of biology do not fall in this
category.
- tractable. This requirement may filter out many problems
(eg related to complex regulatory systems, etc) that may not be
addressed by conjectures amenable to straightforward experimental
verification.
Likewise, we aim to accumulate predictions that provide a precisely
defined and testable functional role, transformation or
interaction. For example, "general class" functional predictions (eg
putative kinase), while being extremely useful, are not in focus of
our effort. Specific predictions can be deduced by various techniques
of comparative and functional genomics. Regardless of the source -
they are valuable additions to HOPS database.
Browsing through examples is arguably the quickest way to grasp the
thrust of HOPS Resource. By launching this site, we commit to populate
it by problems and conjectures emerging from our effort to encode
subsystems in the SEED environment (URL), capturing many aspects of
the Central Machinery of Life. Our goal is to share this information
with the broad scientific community in order to encourage further
computational and experimental analysis. Most importantly, we solicit
community contribution to all three aspects of HOPS Resource, which is
meant to become a joint effort of bioinformaticians and
experimentalists. It is important to emphasize that an experimental
verification of a single gene carefully propagated via
subsystems-based annotations, will often impact a significant number
of genes in a variety of species.