Skype meeting on submission of sorghum terms to Plant Ontology Consortium (POC):
Date: May 12, 2009
Participants:
1. Guy Davenport, CIMMYT (GCP crop ontology)
2. Chih-Wei Tung, TO, Cornell University
3. Pankaj Jaiswal, PO, Oregon State of University
4. Rosemary Shrestha, CIMMYT (GCP crop ontology)
Briefing of the meeting:
The meeting was mainly focused on sorghum terms which were submitted to Plant Ontology Consortium (POC) by GCP chickpea and sorghum ontology developing group (Jayashree Balaji, ICRISAT) during last GCP ontology meeting in Rome. Following conclusions were made in the meeting:
 GCP crop ontology group will give Term IDs as a cross reference for existing terms in TO and PO.
 Trait Ontology (TO) will not include assay/methods and scale. However, GCP ontology group can include them in crop ontology.
 TO will create a sourceforge ticket for new TO term so that GCP crop ontology group can review it.
 TO will record the numbers of terms contributed by GCP crop ontology and mention in the webpage.
Details of Discussion:
1. Flowering time:
a. GCP will keep two child terms of flowering time as in submitted file. However, TO will not include these two terms in their database.
b. Rename the term “flowering time” to “days to flower” and keep the term “flowering time” as a synonym.
c. GCP flowering time related all three terms will be cross ref to TO:0000344.
d. Add "season" after "days to flower: post rainy season " and "days to flower: post rainy season" in OBO-formatted sorghum file.
2. Fungal disease resistance:
a. Cross reference (TO:0000439) should be given to “Fungal disease resistance” term –sorghum group.
b. TO will add the term "sorghum downy mildew resistance" as a single term because TO does not include assays/methods. Therefore, GCP (Sorghum group) need to create generic term "sorghum downy mildew resistance" which will be parent term of GCP_324.0000061 and GCP_324.0000061 terms. New term ID for "sorghum downy mildew resistance" will be used by TO as a cross reference.
c. TO will add "sorghum rust resistance" term and will refer GCP_324.0000063 as a cross reference.
d. TO will add the term "sorghum grain mold" as a child term of TO:0000023 and refer GCP_324.0000064 as a cross reference.

3. Grain related trait:
a. Rename the term "Grain weight over panicle" to "grain weight to panicle weight ratio". This term will be added to TO as a cross reference "GCP_324.0000008".
b. "seed luster" will be added to TO. However, Sorghum group need to clarify whether seed means hulled, polished, non-polished, caryopsis. (Mike may need to find it out..)
c. "seed subcoat" again new term for TO, however, seed coat is present in PO (PO:0020056). Therefore, we need to know what is subcoat? Whether it is testa or tegmen, or something else? (Mike may need to find it out..)
4. Insect damage resistance:
a. Sorghum group will create child term "sorghum shoot fly resistance" which will have two child terms " sorghum shoot fly resistance: rainy season" (pls add season in OBO) and "sorghum shoot fly resistance: post rainy season". This term with new GCP term ID will be then added to TO.
b. TO will add "sorghum stem borer resistance" as a new child term of stem borer resistance and give GCP term ID as a cross reference. Note: I found same term ID GCP_324:0000067 for "sorghum shoot fly resistance: post rainy season" and "sorghum stem borer resistance" terms. Would you please check it again? I hope the mistake is only in my file!
5. Mineral and ion content related trait:
a. Give cross reference term ID for this parent term (TO:0000465).
b. Two terms "shoot sodium content" and "shoot potassium content" will be added in TO and GCP term IDs will be used as cross reference.
6. Panicle related trait:
a. Please check the term “panicle” whether it is used in sorghum for the inflorescence. Pankaj says that most sorghum people use the term “cob” for it.
b. "Panicle length" is exist in TO so sorghum group need to refer TO term ID TO:0000040 as a cross reference.
c. "Panicle exertion: This term is also present in TO with TO:0000165 with spelling "panicle exsertion". Need to correct and give cross reference TO ID to this term by sorghum group. However, TO will modify its existing definition and use GCP definition because it is more appropriate.
d. "Panicle compactness and shape": TO will add this term as a single term and will refer GCP term ID as a cross reference.
7. Stover related trait:
a. TO will add term "stover" as a child term of shoot and will refer GCP term ID as a cross reference.
b. Better to remove “from a pot” from the definition of the term "stover dry weight" to make it generic. TO will add this term as synonym of shoot dry weight (TO:0000552)”.
c. Metabolised energy, Nitrogen digestibility, and Organic matter digestibility, these terms will be added in TO. However, TO needs elaborate definition for these terms. It would be helpful if you provide stover extraction method. Same definition is given for Metabolised energy, and Organic matter digestibility terms except that measurement instrument is mentioned in case of term “Organic matter digestibility “.