planteome / co_331-sweetpotato-traits Goto Github PK
View Code? Open in Web Editor NEWSweetpotato Trait Ontology maintained by Crop Ontology and SweetpotatoBase
Home Page: https://cropontology.org/term/CO_334:ROOT
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co_331-sweetpotato-traits's Issues
Commerical storage root sub categories 'No 1s', 'Jumbos', and 'Canners' used at NCSU are missing from the ontology
Right now we have
CO_331:0000220 'Weight of commercial storage roots measuring kg per plot'
and
CO_331:0000223 'Weight of non-commercial storage roots measuring kg per plot'
NCSU needs further categories within commercial yield for 'No 1s', 'Jumbos', and 'Canners'.
test_trait
Timestamp: 10/23/2017 16:54:37
Crop Name: Sweet Potato
Name of Submitter: test_name
Email: [email protected]
Breeding Program: test_program
Detailed Trait Name: test_trait
Detailed Trait Definition: test_desc
Trait Class: Argonomic
Method of Measurement: test_measuring
Measurement Scale: Unit Measurement (e.g. kg)
List of Categories (comma separated):
Unit of Measurement: test_unit
Storage Root Pithiness
Submitter
| Name | Bryan Ellerbrock |
| Program | Visitor @NCSU |
Request
| Trait Name | Storage Root Pithiness |
| Definition | Pithiness of storage root on a scale of 0-4,. Rated by cutting and visually inspecting 6 marketable roots after close to a full year of storage. |
| Trait Class | Quality |
| Measurement Method | visual rating of storage root pithiness |
| Measurement Type | Categorical |
Categories
| ID | Description |
|---|---|
| 0 | Complete pithiness (large holes) |
| 1 | Severe pithiness (holes, light areas) |
| 2 | Moderate pithiness (no holes, some light areas) |
| 3 | Slight pithiness |
| 4 | No pithiness |
Glucose content of cooked roots in percent
Submitter
| Name | Jolien Swanckaert |
| Program | CIP Ghana |
Request
| Trait Name | Glucose content of cooked roots in percent |
| Definition | Percentage glucose of cooked roots on a dry weight basis |
| Trait Class | Quality |
| Measurement Method | NIRS prediction from calibration derived from standard laboratory analysis after cooking the roots |
| Measurement Type | Unit |
| Measurement Unit | % |
Plant Earliness
Submitter
| Name | Bryan Ellerbrock |
| Program | Visitor @NCSU |
Request
| Trait Name | Plant Earliness |
| Definition | Plant Earliness in beds rated on a scale of 1-3 (late mid early) |
| Trait Class | Agronomic |
| Measurement Method | visual rating |
| Measurement Type | Categorical |
Categories
| ID | Description |
|---|---|
| 1 | Late |
| 2 | Mid |
| 3 | Early |
Sucrose content of cooked roots in percent
Submitter
| Name | Jolien Swanckaert |
| Program | CIP Ghana |
Request
| Trait Name | Sucrose content of cooked roots in percent |
| Definition | Percentage sucrose of cooked roots on a dry weight basis |
| Trait Class | Quality |
| Measurement Method | NIRS prediction from calibration derived from standard laboratory analysis after cooking the roots |
| Measurement Type | Unit |
| Measurement Unit | % |
sweetpotato ontology contact
change contact for sweet potato ontology. Now is Vilma Huala (CIP) and Elisa Sala (CIP)
Pencil type root number
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Number of pencils roots |
| Definition | The number of roots with diameter less than 5 mm per plot |
| Trait Class | Agronomic |
| Measurement Method | Counting the number of roots with diameter less than 5 mm per plot. This measurement was originally taken on I. trifida, a diploid relative of sweetpotato which makes small storage roots. |
| Measurement Type | Unit |
| Measurement Unit | count |
non existing trait
Submitter
| Name | Fake Name |
| Program | fake |
Request
| Trait Name | non existing trait |
| Definition | nothing here to define |
| Trait Class | Abiotic Stress |
| Measurement Method | visual |
| Measurement Type | Categorical |
Categories
| ID | Description |
|---|---|
| 1 | green |
| 2 | red |
There are three traits for "weight of vines" trait:
It's not clear from the names/definitions how these are different. Suggest modifying the names/definitions to make it clear, or get rid of any duplicates. Looks like two of these are actually fresh and dry weight.
[Term]
id: CO_331:0000224
name: sweetpotato weight of vines trait
def: "Weight of vines" [CO:curators]
synonym: "VnW" EXACT []
[Term]
id: CO_331:0000248
name: sweetpotato weight of vines trait
def: "Weight of vines samples" [CO:curators]
synonym: "VnFWt" EXACT []
[Term]
id: CO_331:0000252
name: sweetpotato weight of vines trait
def: "Weight of vines samples" [CO:curators]
synonym: "VnDWt" EXACT []
Vine diameter
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Vine diameter |
| Definition | The diameter of the basal node of the main vine |
| Trait Class | Morphological |
| Measurement Method | The average diameter of basal nodes measured on the main vine of representative plants per plot |
| Measurement Type | Unit |
| Measurement Unit | mm |
Vine lenght
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Vine length |
| Definition | The main vine is measured at certain time-point |
| Trait Class | Morphological |
| Measurement Method | The average length of of the main vine of representative plants per plot is measured. |
| Measurement Type | Unit |
| Measurement Unit | cm |
add method and scale to the variable Storage root total marketable yield weight computation tons per ha
Here the variable:
[Term]
id: CO_331:0000814
name: Storage root total marketable yield weight computation tons per ha
def: "Marketable root yield" []
synonym: "RtCYld_Cp_tha" EXACT []
synonym: "RYTHA" EXACT []
relationship: variable_of CO_331:0000307 ! marketable root yield
created_by: W. Grueneberg
creation_date: 2016-11-30T21:23:23Z
For the scale, use this id CO_331:0000897
Keep Advantages
Submitter
| Name | Bryan |
| Program | NCSU |
Request
| Trait Name | Keep Advantages |
| Definition | A trait to track what advantages an accession has that leads to it being selected. |
| Trait Class | Morphological |
| Measurement Method | visual |
| Measurement Type | Categorical |
Categories
| ID | Description |
|---|---|
| GoodAT | Good Attachment |
| Blocky | Blocky root shapes |
| Early | Sizes up early, early maturity |
| GDSizeDist | Good size distribution |
| HighDM | High Dry Matter |
| HighSet | Lots of roots |
| Proc_Only | Not a good for fresh market, only processing |
| Round | Roots are round |
| ShapeUnifo | Shapes are fairly uniform |
Canopy Temperature
Submitter
| Name | Dorcus Gemenet |
| Program | CIP |
Request
| Trait Name | Canopy Temperature |
| Definition | Measurement using an infrared thermometer on the canopy of a plot |
| Trait Class | Physiological |
| Measurement Method | Measurement using an infrared thermometer on the canopy of a plot |
| Measurement Type | Unit |
| Measurement Unit | 0C |
add method and scale to the variable Storage Root Defects secondary estimating 1-18
Here, the variable:
[Term]
id: CO_331:0000813
name: Storage Root Defects secondary estimating 1-18
def: "Type and/or name of secondary visible storage root defect. 1 = Blisters (BLI), 2 = Tea Staining (TEA), 3 = Air Cracking (AIR), 4 = Bumpy (BUM), 5 = Cracking (CRA), 6 = Early Season Cracking (ESC), 7 = Grooves (GRV), 8 = Insect Damage (INS), 9 = Excessive Latex (LTX), 10 = Skinning (SKN), 11 = Sprouts (SPR), 12 = Striations (STR), 13 = Tails (TLS), 14 = Veins (VNS), 15 = Deep Eyes (DES), 16 = Misshapes (MIS), 17 = Secondary Roots (SRS), 18 = Tight Hills (THS)." []
synonym: "RTDEF2" EXACT []
synonym: "RtDefS_Et_1to18" EXACT []
relationship: variable_of CO_331:0000812 ! storage root defects (secondary)
created_by: C. Yencho
creation_date: 2016-11-30T20:44:25Z
Test Trait 1
Submitter
| Name | David |
| Program | BTI |
Request
| Trait Name | Test Trait 1 |
| Class | Morphological |
| Definition | This is a test description |
| Measurement Method | tested it. |
| Measurement Type | Categorical |
Categories
| ID | Description |
|---|---|
| A | desc1 |
| 2 | desc2 |
| 3 | desc3 |
add a photo trait to the ontology
The sweetpotato breeding program at NCSU takes photos using the fieldbook app, along with traits currently in the ontology. Should a photo trait be considered part of the ontology?
Plants Available
Submitter
| Name | Bryan Ellerbrock |
| Program | Visitor @NCSU |
Request
| Trait Name | Plants Available |
| Definition | Plants Available in bed measured in number of plants counted |
| Trait Class | Agronomic |
| Measurement Method | counting |
| Measurement Type | Unit |
| Measurement Unit | plants |
reaction to streptomyces soil rot in greenhouse
Submitter
| Name | Streptomyces soil rot greenhouse rating |
| Program | Visitor @NCSU |
Request
| Trait Name | reaction to streptomyces soil rot in greenhouse |
| Definition | A trait already exists for 'reaction to streptomyces soil rot' CO_331:0000419 , but it does not adequately describe the multiple ratings that can be taken. |
| NCSU rates SSR on a 0-4 scale on roots in the field, then also does an assay rating SSR on stems in the greenhouse. Not sure if this should be covered by one trait with different methods, or two separate traits. | |
| Trait Class | Biotic Stress |
| Measurement Method | visual rating of SSR symptoms |
| Measurement Type | Categorical |
Categories
| ID | Description |
|---|---|
| 0 | Susceptible |
| 1 | Moderately Susceptible |
| 2 | Moderately Resistant |
| 3 | Resistant |
| 4 | Highly Resistant |
Plant Production
Submitter
| Name | Plant Production |
| Program | Visitor @NCSU |
Request
| Trait Name | Plant Production |
| Definition | Plant production in beds rated from 0-9 (none-profuse) |
| Trait Class | Agronomic |
| Measurement Method | visual rating |
| Measurement Type | Categorical |
Categories
| ID | Description |
|---|---|
| 0 | None |
| 9 | Profuse |
CO_331:0000218 id is duplicated
CO_331:0000218 is used as the id for both Storage root total marketable yield weight computation tons per ha and Weight of commercial storage roots. This is causing a conflict in sweetpotatobase (and maybe is also why the Weight of commercial storage roots trait is not visible on crop ontology?)
How can this be resolved? Weight of commercial storage root data is already stored in sweetpotatobase, so the temporary solution has been to exclude Storage root total marketable yield weight computation tons per ha from the working obo file.
Storage Root Defects CO_331:0000423 needs to be re-worked
An abiotic stress trait called Storage Root Defects was added in the most recent version of the ontology. It's a categorical trait on a 14pt scale. Each category represents a different type of defect (Blisters (B), Sprouts (SPR), etc).
We've encountered a few problems with this setup. Defining the trait this way only allows you to select one defect, even though there are often multiple defects. And the 14pt scale is too large for the fieldbook app - any more than 12 categories causes it to crash.
This system also overlaps in strange ways with other traits. It's classified as an abiotic stress trait, but Category 8 is for insect damages, a biotic stress trait. And existing traits classified as Agronomic ( CO_331:0000097 Storage root cracking) and Morphological ( CO_331:0000326 Storage Root Surface Defects ) already cover many of the same defects.
test_t
Timestamp: 10/23/2017 16:59:10
Crop Name: Sweet Potato
Name of Submitter: Another_tester
Breeding Program: test_p
Detailed Trait Name: test_t
Detailed Trait Definition: test_d
Trait Class: Biotic Stress
Method of Measurement: test_m
Measurement Scale: Unit Measurement (e.g. kg)
List of Categories:
Unit of Measurement: test_u
Trait names 'Weight of vines' and 'Weight of storage root' are also duplicated
These name duplications prevented the ontology from loading into sweetpotatobase. Looking at the defintions, they are distinct traits using measurements of dry and fresh weights, so to load them I changed
CO_331:0000224 Weight of vines CO_331:0000240 Weight of storage root CO_331:0000244 Weight of storage root CO_331:0000248 Weight of vines CO_331:0000252 Weight of vines
to
CO_331:0000224 Weight of vines CO_331:0000240 Fresh Weight of storage root CO_331:0000244 Dry Weight of storage root CO_331:0000248 Fresh Weight of vines CO_331:0000252 Dry Weight of vines
in the working obo file.
Pencil type root fresh weight
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Pencil roots fresh weight |
| Definition | The weight of roots with diameter less than 5 mm |
| Trait Class | Agronomic |
| Measurement Method | Weighing the total roots per plot with diameter less than 5 mm |
| Measurement Type | Unit |
| Measurement Unit | g |
Starch content of cooked roots in percent
Submitter
| Name | Jolien Swanckaert |
| Program | CIP Ghana |
Request
| Trait Name | Starch content of cooked roots in percent |
| Definition | Percentage starch of cooked roots on a dry weight basis |
| Trait Class | Quality |
| Measurement Method | NIRS prediction from calibration derived from standard laboratory analysis after cooking the roots |
| Measurement Type | Unit |
| Measurement Unit | % |
Plant Uniformity
Submitter
| Name | Bryan Ellerbrock |
| Program | Visitor @NCSU |
Request
| Trait Name | Plant Uniformity |
| Definition | Plant uniformity while emerging from beds, measured from 0-9 (highly variable to uniform) |
| Trait Class | Agronomic |
| Measurement Method | visual rating |
| Measurement Type | Categorical |
Categories
| ID | Description |
|---|---|
| 0 | highly variable |
| 9 | uniform |
CO_331:0000718 definition does not match name and synonyms
Is it a temperature or a salt trait?
| Term id | CO_331:0000718 |
|---|---|
| Term name | Reaction to high soil temperature estimating 1-9 |
| Term definition | Response of a plant to damage by high concentration salt. 1 = Very low, 3 = Low, 5 = Intermediate, 7 = High, 9 = Very High |
| Comment |
Synoyms
RnSTp_Et_1to9
SOILTEMP
"RnSTp_Et_1to9" EXACT []
"SOILTEMP" EXACT []
Leaf area index
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Leaf area index |
| Definition | Leaf area index estimated from image analysis of standard pictures taken of representative leaves per plot and anlyzed usign any image analysis software |
| Trait Class | Morphological |
| Measurement Method | Image analysis of pictures taken from representative mature leave per plot. Is very important to consider the same light conditions, distance and time while taking pictures in order to avoid plot to plot variation. |
| Measurement Type | Unit |
| Measurement Unit | mm2 |
Best way to handle the same biochemicals traits measured at multiple time points?
The sweetpotato program at NCSU, as well as programs in Ghana and Uganda, is using NIRS to measure the new biochemical traits recently added to the ontology (Amylose, Anthocyanin, etc). But these traits aren't just measured once, they're done first on green samples, then cured samples, then at 6 weeks, 12 weeks, and so on. What is the best way of handling these measurements? There's interest in storing and analyzing them as separate measurements, but also in calculating an overall value for each compound.
obo file formatting problems
format of traits and variables in cropontology.org obo download (http://www.cropontology.org/obo/CO_331):
[Term]
id: CO_331:0000069
name: Storage Root Shape (primary)
namespace: Sweet PotatoTrait
def: "undefined" []
namespace: Sweet PotatoScale
relationship: scale_of CO_331:Morphological%20trait
[Term]
id: CO_331:0000774
name: RtShpP_Et_1to8
synonym: "RTSHP1" EXACT []
namespace: SweetpotatoVariable
relationship: variable_of CO_331:0000069
format needed for sweetpotatobase (and other sgn databases):
[Term]
id: CO_331:0000069
name: Storage Root Shape (primary)
namespace: SweetpotatoTrait
def: "Storage Root Shape described from longitudinal sections made about the middle of freshly harvested storage roots" [Huaman1991:Def_4.2.1]
comment: | Entity: Root | Attribute: Shape | Trait status: Recommended.
synonym: "RtShpP" EXACT []
is_a: CO_331:0000002 ! Morphological trait
[Term]
id: CO_331:0000774
name: Storage Root Shape primary estimating 1-8
namespace: SweetpotatoTrait
def: "Storage Root Shape described from longitudinal sections made about the middle of freshly harvested storage roots" [Huaman1991:Def_4.2.1]
synonym: "RTSHP1" EXACT []
synonym: "RtShpP_Et_1to8" EXACT []
relationship: variable_of CO_331:0000069 ! Storage Root Shape (primary)
number of commercial roots per plant (ncrpp)
Submitter
| Name | Jolien Swanckaert |
| Program | CIP Ghana |
Request
| Trait Name | number of commercial roots per plant (ncrpp) |
| Definition | number of commercial roots per plant, number of commercial roots per plot (CO_331:0000214) divided by number of plants harvested (CO_331:0000679) |
| Trait Class | Agronomic |
| Measurement Method | calculation |
| Measurement Type | Unit |
| Measurement Unit | number |
Question about trait: CO_331:0000408 'Appearance of hearbarium'
It's not clear what this trait is referring to- is it the whole plant appearance?
Keep/Drop trait
I don't see a trait for this yet in the ontology, but the NCSU program uses a boolean trait they call KEEP?DROP in their fieldbooks in the early stages of the breeding process. This trait is recorded first, and for most genotypes that are dropped it is not worth recording values for the remaining traits.
Fructose content of cooked roots in percent
Submitter
| Name | Jolien Swanckaert |
| Program | CIP Ghana |
Request
| Trait Name | Fructose content of cooked roots in percent |
| Definition | Percentage fructose of cooked roots on a dry weight basis |
| Trait Class | Quality |
| Measurement Method | NIRS prediction from calibration derived from standard laboratory analysis after cooking the roots |
| Measurement Type | Unit |
| Measurement Unit | % |
Agronomic trait 'yield of total roots' is duplicated
The ids, synonyms, and are Xrefs are different (CO_331:0000082 RtYld Grueneberg2010:Def_38 vs
CO_331:0000309 RtYPP Grueneberg2016:Def_46 ) so I named the second one 'yield of total roots 2` in our working file so I could at least load it.
But the defintion, method, and scale seem to be the same, maybe they should be merged instead?
Leaf area
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Leaf area |
| Definition | The leaf area measurement based on a number of representative leaves per plot |
| Trait Class | Morphological |
| Measurement Method | Image analysis of pictures taken on representative mature leaves per plot. The picture taking should be under controlled conditions to avoid variations from one plot to the next. |
| Measurement Type | Unit |
| Measurement Unit | mm2 |
Maltose content of cooked roots in percent
Submitter
| Name | Jolien Swanckaert |
| Program | CIP Ghana |
Request
| Trait Name | Maltose content of cooked roots in percent |
| Definition | Percentage maltose of cooked roots on a dry weight basis |
| Trait Class | Quality |
| Measurement Method | NIRS prediction from calibration derived from standard laboratory analysis after cooking the roots |
| Measurement Type | Unit |
| Measurement Unit | % |
Canopy temperature
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Canopy temperature |
| Definition | The temperature of the canopy measured using an infrared thermometer |
| Trait Class | Physiological |
| Measurement Method | The average recorded value of canopy temperature made by passing the infrared thermometer on canopies of representative plants per plot |
| Measurement Type | Unit |
| Measurement Unit | Degrees centigrade |
Virus symptoms 2 definition is incomplete
Missing explanation of 1-9 scale
Consider using protege csv plugin to save ontology edits in both obo and csv format
add method and scale to the variable Overall storage root disease symptoms estimating 1-9
Here, the variable:
[Term]
id: CO_331:0000816
name: Overall storage root disease symptoms estimating 1-9
def: "Overall storage root disease symptoms evaluation. 1=Very poor, 3 = Poor, 5 = Moderate, 7 = Good, 9 = No disease" []
synonym: "DISEASE" EXACT []
synonym: "RtDSm_Et_1to9" EXACT []
relationship: variable_of CO_331:0000815 ! overall storage root disease symptoms
created_by: C. Yencho
creation_date: 2016-12-01T04:02:09Z
name1
Timestamp: 10/23/2017 17:02:24
Crop Name: Sweetpotato
Name of Submitter: test_3
Breeding Program: bp
Detailed Trait Name: name1
Detailed Trait Definition: oh yay
Trait Class: Morphological
Method of Measurement: method
Measurement Scale: Categorical Measurement (e.g. [1: worst, 2, 3, 4, 5: best] or [yellow, green, purple] )
List of Categories: 1:a,2:b,3:c
Unit of Measurement:
Relative Chlorophyll Content
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Relative Chlorophyll Content |
| Definition | The indirect measure of Chlorophyll content using SPAD readings |
| Trait Class | Physiological |
| Measurement Method | The average of SPAD readings taken on representative plants per plot using SPAD meters |
| Measurement Type | Unit |
| Measurement Unit | nmol |
Mature Leaf Size
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Mature Leaf Size |
| Definition | The average size of the leaves estimated by measuring representative mature leaves per plot |
| Trait Class | Morphological |
| Measurement Method | Measuring the length of representative mature leaves per plot from the base to the tip and taking the average plot reading |
| Measurement Type | Unit |
| Measurement Unit | cm |
average commercial root weight (acrw)
Submitter
| Name | Jolien Swanckaert |
| Program | CIP Ghana |
Request
| Trait Name | average commercial root weight (acrw) |
| Definition | average commercial root weight, commercial root weight divided by number of commercial roots |
| Trait Class | Agronomic |
| Measurement Method | calculation |
| Measurement Type | Unit |
| Measurement Unit | kg |
Petiol size
Submitter
| Name | Mosquera, V |
| Program | CIP-Lima |
Request
| Trait Name | Petiol length |
| Definition | The average length of the petiole measured on representative mature leaves per plot |
| Trait Class | Morphological |
| Measurement Method | Length of the petiole defined as the distance between the vine node and the basal lobe of the leaf. The average of representative plants is taken as the plot reading |
| Measurement Type | Unit |
| Measurement Unit | cm |
Overall Disease Trait
NCSU uses a trait called Disease, with scale
1=Very poor; 3 = Poor; 5 = Moderate; 7 = Good; 9 = No disease
where they don't identify the specific disease, or identify it in a separate comment. At the moment there is no corresponding trait in the ontology.
Total Bed Production
Submitter
| Name | Bryan Ellerbrock |
| Program | Visitor @NCSU |
Request
| Trait Name | Total Bed Production |
| Definition | Total Bed Production in estimated number of plants |
| Trait Class | Agronomic |
| Measurement Method | estimation |
| Measurement Type | Unit |
| Measurement Unit | plants |
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