Add section on colony morphology phenotypes to 'phenotype tips'

[CuzickA]

Based on below from Val 16_11_2020

Useful sections from

https://academic.oup.com/bioinformatics/article/29/13/1671/200708

At the broadest level of classification, FYPO organizes terms along three axes. One axis distinguishes normal from abnormal phenotypes, where ‘normal’ is operationally defined as indistinguishable from characteristics of cells isogenic to the sequenced wild-type strain (972 h−), and ‘abnormal’ as detectably different from wild type, under the conditions in which a phenotype is assessed in a particular experiment.
A second axis classifies phenotypes by the entity affected; the broad categories correspond to effects on biological processes (as defined in GO), molecular functions (GO) or cellular structures (corresponding to GO cellular components). The third axis distinguishes phenotypes relevant at the level of a cell are from those that can be observed only in a population of cells.
2.2.3 Phenotype modeling challenges
FYPO also includes a number of terms that do not fit the simple logical models described above. The principal types are complex phenotypes, which encompass more than one quality, and phenotypes that affect cell populations……..
Although most fission yeast phenotypes can be represented as properties of a cell (including events taking place in a cell), some phenotypes can only be observed at the level of a population. These cell population phenotypes reflect properties of what cells do in groups, and pose particular challenges for logical modeling because they do not represent characteristics of a single organism. Some examples are colony morphology (‘abnormal colony morphology’ FYPO:0000150), flocculation (‘flocculating cells’ FYPO:0000155) and filament morphology. Some cellular processes can also be studied in cell populations, giving rise to population-level phenotype observations; one example is septation, for which the ‘septation index’, i.e. the proportion of cells in a population observed undergoing septation under given conditions is often measured. Although FYPO:0000155 is defined as ‘increased occurrence’ (PATO:0002051) of ‘flocculation’ (GO:0000128), most cell population phenotype terms are among the small fraction in FYPO that do not yet have logical definitions.
To accurately model some phenotypes has required the introduction of a few relations that are not defined in the OBO Relations Ontology (RO; http://code.google.com/p/obo-relations/) or the Basic Formal Ontology (BFO; http://www.ifomis.org/bfo/) at present. Some, such as during and its subtypes exists_during and happens_during, which are used to link process or structural phenotypes to periods such as cell cycle phases, are borrowed from a set of relations developed by the GO Consortium for its annotation extensions (Huntley et al., manuscript in preparation). Others, such as includes_cells_with_phenotype, which links cell population phenotypes with cell-level phenotypes of cells within the population, have been created specifically for FYPO and will be submitted as candidates for addition to RO.

So in PHIPO we:

1. Followed the approach above for population phenotypes, with descendant terms for yeast forms and hyphal forms where appropriate
2. However, colony size has different meanings for yeast (population size/population growth) and for hyphal forms (individual growth via increased size of an individual by either hyphal extension or branching).

We, therefore, omitted a grouping term “colony size phenotype”, because these represent different obsevations and included only a term for “hyphal colony size phenotype”, referring to the growth of an individual. Yeast colony size phenotypes are annotated using the population growth terms because they refer to the increase of a population.