Goal 3. Wood qualities and phenotypes
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Back to the main Agenda page: Wood_anatomy_ontology_meeting,_2012_at_NYBG,_agenda
Neighboring ontologies of the PO: Describing Traits and Phenotypes
Unlike goals 1 and 2, this goal goes beyond the current domain of the PO, but as we discussed in the sessions, we are closely linked to the Trait Ontology and utilize the PATO extensively.
Each of these have their own SourceForge trackers and repositories.
Background
- What is a trait? What is a quality?
- What is the difference between an entity and a phenotype?
- How do the TO and PATO differ from the PO? How are they similar? How do they interact?
For more explanations, please see: File:PO Walls wood meeting short.pdf
Domain of Trait Ontology (TO)
The Trait Ontology is hosted by Gramene.
The TO consists of precomposed terms to describe each trait as a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature individual. TO is specific to plants (should be called Plant Trait Ontology).
Examples are glutinous endosperm, disease resistance, plant height, photosensitivity, male sterility, etc.
The TO is organized around 9 main parent terms or categories:
Domain of Phenotypic Quality Ontology (PATO)
PATO is an ontology of phenotypic qualities, intended for use in a number of applications, primarily defining composite phenotypes and phenotype annotation and is applicable to all organisms.
From PATO Wiki:
PATO is an ontology of *phenotypic qualities*, intended for use in a number of applications, primarily phenotype annotation.
The new PATO differs from the old in that the system of attributes and values has been abandoned in favor of a single hierarchy of qualities.
PATO is designed to be used in conjunction with ontologies of "quality-bearing entities". An example of such an entity is an insect eye (taken from the fly_anatomy ontology), which could be the bearer of the quality 'red' (PATO:0000322). This combination is the "red eye" phenotype.
We say that the phenotype term is 'post-coordinated', as it is formed by coordinating two terms together. This is in contrast to ontologies of pre-coordinated phenotypes, such as the Mammalian Phenotype (MP) ontology. See below for a more formal treatment.
Other ontologies of content bearers include the OBO Cell ontology (CL), the GO biological process or cellular component ontologies, and ontologies of anatomical entities (such as the PO).
Describing wood traits, qualities and phenotypes:
Priorities: User needs and accessing genomic data:
- How should we prioritize which traits are the most important, which to focus on first?
-ones used in the literature, to describe QTL or transcriptome datasets
- Wood traits for which genomic data are currently being collected should be a priority:
- AG will contact some of the other database groups and survey which terms they are using: see below
From AG: "The 'biofuel' biochemical traits and basic measures of wood development and quality are the ones that will have the most genetic and genomic data associated with them. Some of the more derived traits that are in the long list that have to do with wood physical properties are more used by wood physical scientists and engineers, and not so much by geneticists. I can't think of any datasets looking at the genetics of board checking, gluing properties, and those sorts of traits."
- How will quality/phenotype terms be used and by who? Will we develop annotations to them and where will they be stored?
- Are we creating a separate "Wood Quality Ontology" versus describing phenotypes on the fly using cross products?
List of terms needed
See link to Google Doc for wood traits
At the Workshop we started compiling a list (in Google doc) of trait and quality terms from various sources and tried to categorize them based the nine main headings of the TO.
Sources:
List from BL: Media:WQ traits (BL 2-6-12) .pdf
List from AW: Media:Andrew_Wood_traits_mapped_to_TO_Sheet1.pdf
List from MS:
Database groups:
TRY Database
A global database of plant traits
See link to the Core traits and related data they are interested: link
ORNL Plant Genomics Group
Bioenergy traits measured on (primarily) Populus: Wet weight core + bark
Wet weight core
Dry weight core
Wet weight bark
Dry weight bark
Diameter with bark
Diameter without bark
Wet thickness
Dry thickness
Water displacement of core
Wood Science, University of British Columbia
Shawn Mansfield and Carl Douglas, Wood and Fibre Quality Department
Fibre length
Fibre width
Wood density
Wood microfibril angle
Cell wall crystallinity
Total lignin
Acid soluble lignin
Acid insoluble lignin
Lignin S:G ratio
Arabinose
Rhamnose
Galactose
Glucose
Xylose
Mannose
Alpha Cellulose
Holocellulose
Acetate content
Any any ratio of the above
PopGenie.org
Nathaniel Street, Umea, Sweden
List of traits measured for QTL and association mapping studies at UPSC:
Stem diameter
Stem height
Stem volume
Wood density
Wood stiffness
Xylem vessel width (angiosperms)
Xylem vessel length (angiosperms)
Xylem vessel cell wall thickness (angiosperms)
Xylem fiber width (angiosperms)
Xylem fiber length (angiosperms)
Xylem fiber cell wall thickness (angiosperms)
Tracheid width (gymnosperms)
Tracheid length (gymnosperms)
Tracheid cell wall thickness (gymnosperms)
Radial width of the living xylem
Microfibril angle
Total lignin content
S/G lignin ratio
Total carbohydrate content
Total extractives content
Amount of cellulose
Cellulose crystallinity
Degree of cellulose polymerisation
Amount of xylan
Amount of soluble sugars (glucose, fructose, saccharose)
Amount of uronic acids Sugar release during saccharification
Existing glossaries:
See list of links at Inside Wood site: IAWA glossaries
References from literature:
Sannigrahi, P., Ragauskas, A.J., and Tuskan, G.A. (2010). Poplar as a feedstock for biofuels: A review of compositional characteristics. Biofuels, Bioprod. Bioref. 4, 209–226. link
To do:
- We will do preliminary edits to the TO for wood traits, depending upon the priorities for the PO and TO
- Survey other database groups about terms needed in the TO/Plant Ontology- AG: see info above, JW will also follow up with some she works with
- Prioritize the list of trait and quality terms by user need, access to genomic data, commercial importance: add these to the TO by September 2012 (LC)
- Work with GO to get terms needed for wood traits, based on priorities above (LC, others?)
- Work with ChEBI to get terms needed for wood chemical compounds
- Add measurements to trait ontology (focus on the wood) '???
- Add biofuel traits from the Sannigrahi et al (2010), Poplar paper
- Consult with domain experts about how traits are measured eg. specific plant diseases
Notes and questions that came up:
- fiber in pulp and paper can include any type of cell, e.g. "pulp fiber" not the same as "fiber cell"
- susceptibility vs resistance are two sides of the same trait or are they?
- Is the lignin network part of the cell (GO) or is it extracellular (belongs in PO)?? See above
- What should be done about concerns over TO general structure?
