Difference between revisions of "Plant Stress Ontology"
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| − | Plant Stress Ontology (PSO): The PSO will describe both major types of stress: abiotic (drought, salinity, temperature, nitrogen deficiencies, etc.) and biotic (pests, pathogens, symbiotic organisms, competition, diseases, etc.), which will form the two main branches of the PSO. | + | '''Plant Stress Ontology (PSO):''' The PSO will describe both major types of stress: abiotic (drought, salinity, temperature, nitrogen deficiencies, etc.) and biotic (pests, pathogens, symbiotic organisms, competition, diseases, etc.), which will form the two main branches of the PSO. |
| − | The PSO design will model the stresses by developing a super network of ontology nodes | + | The PSO design will model the stresses by developing a super network of ontology nodes imported from other cROP and reference ontologies using a MIREOT strategy and designating the appropriate edges (relationships) between the terms. |
The approach would include identification of the first set of terms (entities) and normalizing them with experimental evidences, detecting related pairs, predicting the events and finally network extraction. This will be followed by a manual quality checks by experts. | The approach would include identification of the first set of terms (entities) and normalizing them with experimental evidences, detecting related pairs, predicting the events and finally network extraction. This will be followed by a manual quality checks by experts. | ||
| − | Each major stress branch will include a hierarchy of terms describing different types of stress. The same sub branches will integrate inter-ontology network with appropriate term-term relationships. These networks will inform about the genetic level functions and processes, symptoms (phenotypes), environments, affected plant structures and the growth stages of the plant species which are associated for a given stress | + | Each major stress branch will include a hierarchy of terms describing different types of stress. The same sub branches will integrate inter-ontology network with appropriate term-term relationships. These networks will inform about the genetic level functions and processes, symptoms (phenotypes), environments, affected plant structures and the growth stages of the plant species which are associated for a given stress. |
| − | We will interact with the CO group and various CGIAR projects | + | We will interact with the CO group and various CGIAR projects to develop this network. However, a greater part of the PSO network will be driven by the statistical network calculations based on the annotations of the data nodes involving stress response phenotypes displayed by a host plant while interacting with its growth environment. The biotic stress branch will incorporate the Plant Infectious Disease Ontology (IDOPlant), a conceptual model developed recently. |
| − | The goals of IDOPlant were to provide plant scientists with the means to identify genomic and genetic signatures of host pathogen interactions, resistance, or susceptibility, and to help agronomists and farmers by developing tools to identify disease phenotypes and gather epidemiological statistics | + | The goals of IDOPlant were to provide plant scientists with the means to identify genomic and genetic signatures of host pathogen interactions, resistance, or susceptibility, and to help agronomists and farmers by developing tools to identify disease phenotypes and gather epidemiological statistics. The biotic stress branch will include the most widely-studied plant crop diseases such as bacterial blight and blast (rice), rust and scab (cereal crops), smut (soybean and other legumes), and other diseases as prioritized and selected by our collaborators. |
Emphasis will also be given to the type of stress for which a large-scale data exists and/or is in the process of being generated, to enable metagenomics (of interest to DOE-KnowledgeBase) and ecological studies. The plant abiotic stress branch will be similarly modeled with priorities on stresses like drought, salinity, nitrogen and temperature. | Emphasis will also be given to the type of stress for which a large-scale data exists and/or is in the process of being generated, to enable metagenomics (of interest to DOE-KnowledgeBase) and ecological studies. The plant abiotic stress branch will be similarly modeled with priorities on stresses like drought, salinity, nitrogen and temperature. | ||
Revision as of 16:39, 13 May 2013
Plant Stress Ontology (PSO): The PSO will describe both major types of stress: abiotic (drought, salinity, temperature, nitrogen deficiencies, etc.) and biotic (pests, pathogens, symbiotic organisms, competition, diseases, etc.), which will form the two main branches of the PSO.
The PSO design will model the stresses by developing a super network of ontology nodes imported from other cROP and reference ontologies using a MIREOT strategy and designating the appropriate edges (relationships) between the terms.
The approach would include identification of the first set of terms (entities) and normalizing them with experimental evidences, detecting related pairs, predicting the events and finally network extraction. This will be followed by a manual quality checks by experts.
Each major stress branch will include a hierarchy of terms describing different types of stress. The same sub branches will integrate inter-ontology network with appropriate term-term relationships. These networks will inform about the genetic level functions and processes, symptoms (phenotypes), environments, affected plant structures and the growth stages of the plant species which are associated for a given stress.
We will interact with the CO group and various CGIAR projects to develop this network. However, a greater part of the PSO network will be driven by the statistical network calculations based on the annotations of the data nodes involving stress response phenotypes displayed by a host plant while interacting with its growth environment. The biotic stress branch will incorporate the Plant Infectious Disease Ontology (IDOPlant), a conceptual model developed recently.
The goals of IDOPlant were to provide plant scientists with the means to identify genomic and genetic signatures of host pathogen interactions, resistance, or susceptibility, and to help agronomists and farmers by developing tools to identify disease phenotypes and gather epidemiological statistics. The biotic stress branch will include the most widely-studied plant crop diseases such as bacterial blight and blast (rice), rust and scab (cereal crops), smut (soybean and other legumes), and other diseases as prioritized and selected by our collaborators.
Emphasis will also be given to the type of stress for which a large-scale data exists and/or is in the process of being generated, to enable metagenomics (of interest to DOE-KnowledgeBase) and ecological studies. The plant abiotic stress branch will be similarly modeled with priorities on stresses like drought, salinity, nitrogen and temperature.
