wiki:FYPOContentStructure

FYPO Content and Structure

Introduction

FYPO defines a phenotype as an observable characteristic, or set of characteristics, of an organism that results from the interaction of its genotype with a given environment.

Wherever practical, FYPO terms have entity--quality (EQ) logical definitions (see Mabee et al. 2007 and Mungall et al. 2010) that refer to PATO qualities and follow the PATO XP best practices. The entity may be whole cell, a population of cells, a part of a cell (corresponding to a GO cellular component), or an event such as a molecular function or biological process (represented by GO terms). An entity specification can be further refined with additional details using GO or ChEBI terms. Representative examples are available.

FYPO includes many highly detailed pre-composed terms. The primary motivation is to facilitate literature curation by fission yeast community researchers, who will likely want to annotate to highly specific terms. For bench biologists, the simpler procedure of annotating to a single pre-composed term is more intuitive than the parallel annotation process required with post-composition. Experimental conditions are usually not used in FYPO term pre-composition. A few exceptions and outstanding issues are noted on the phenotype pre- vs. post-composition wiki page.

High-level organization

FYPO uses six top-level classes, reflecting three axes of classification (normal/abnormal; biological process/molecular function; cell/cell population).

Normal and abnormal phenotypes

In FYPO "normal" (FYPO:0000257) is operationally defined as indistinguishable from characteristics of cells isogenic to the sequenced wild type strain (972 h-), and "abnormal" (FYPO:0001985) as detectably different from wild type, under the conditions in which a phenotype is assessed in a particular experiment.

Process and function phenotypes

Biological process phenotype (FYPO:0000300): Any phenotype in which the affected entity corresponds to a GO biological process (GO:0008150). For fission yeast, most phenotypes affect processes at the level of a single cell (GO:0044763, single-organism cellular process), with a few exceptions.

Molecular function phenotype (FYPO:0000652): Any phenotype in which the affected entity corresponds to a GO molecular function (GO:0003674). Molecular function phenotypes are usually interpreted as characteristics of the activity observed in (or recovered from) a cell or population of cells, compared to wild type cells.

Note: On PomBase gene pages, all molecular function phenotypes and most biological process phenotypes are displayed under the "cell phenotype" heading, although neither "molecular function phenotype" nor "biological process phenotype" is itself classified as a cell phenotype.

Cell and population phenotypes

Cell phenotype (FYPO:0000002): Any phenotype that is observed at the level of an individual cell. The cell phenotype branch encompasses cell-level processes (as noted above) as well as phenotypes that affect the physical qualities of a cell or its parts (FYPO:0000136, cellular physical quality phenotype). Phenotype affecting cell parts refer to GO cellular component (GO:0005575) terms as entities.

Cell population phenotype (FYPO:0000003): Any phenotype that is observed at the level of a population of cells. Certain phenotypes, such as colony morphology (e.g. FYPO:0000150) or septation index (the proportion of a population that contain septa; e.g. FYPO:0000650), exist only in cell populations, not in single cells. Other cell population phenotypes affect entities that correspond to biological processes involving more than one organism (GO:0044764, multi-organism cellular process).

The cell population phenotype branch of FYPO also includes terms for viability and growth at the level of cell populations, as described below.

Viability and growth

Any individual cell is viable or inviable, and a viable cell may grow, or not grow, under a given set of conditions. In fission yeast (as in most most microorganisms), however, experiments to assay viability or the rate or extent of growth are far more commonly done at the level of cell populations. For example, the rate of cell population growth may be measured in a cell culture, or the extent of growth may be observed on plates. Furthermore, many mutations in S. pombe cause some, but not all, cells with the mutation to die. For example, the penetrance of "cut" (FYPO:0000229) is often 10% or less. Thus, even though each individual "cut" cell is inviable, the population is viable.

Although annotation to a cell phenotype plus an extension to indicate penetrance would be at least semantically equivalent (if not more specific), quantitative penetrance data are often unavailable for curation. At present, it is also prohibitively difficult to query the penetrance data that have been captured with annotation extensions. Annotations to cell population viability terms allow PomBase users to tell whether they can expect cells with a given mutation to grow.

Last modified 5 years ago Last modified on Jun 3, 2015, 2:44:18 PM