Revision as of 18:43, 13 June 2016

Planteome Ontology WG Zoom Meeting

Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/132105144

Brandon Sinn has joined Dennis Stevenson's group at the NYBG

Brief biography from Brandon: I received my Ph.D. in December 2015 from Ohio State University, under the supervision of Dr. John Freudenstein. My dissertation focused on phylogenetics, character-associated diversification, species delimitation, and organellar genome evolution in the genus Asarum (Aristolochiaceae).

Update from Brandon and Dennis on their work:
- Planteome Goal: Develop ontologies required for annotating and describing the experiments, data sets, tagging published papers, and images.
- We are augmenting the PO with taxon neutral, but specialized terms required for accurate annotation or genes and visual aids.
- We will be doing this in an integrated systems approach where we start in the stem and work our way into all other organs. Currently sorting through stele types. We will next move to roots.
- We plan to work up PO-annotated life cycle diagrams

- Generating visual aids for ontological terms for taxa that currently have genome annotations accessible in the Planteome portal, and their relatives and for Wild-type models and their relatives:
  - Macro-scale organs for use by individuals in the field or interested citizen scientists or students
  - High resolution scans of pertinent illustrations and line drawings from pre-copyright books and peer-reviewed literature.
  - Histological preparations from these targeted taxa, tissues and organs for annotation in the PO.
  - Curating, imaging, and incorporating historic liquid-preserved anatomical collections housed at the NYBG: Stevenson, Chamberlain, Ericaceae

Questions:
- Brandon is interested in helping to annotate orphan genomes and the maintenance of reference genome annotations (goal 2.3 from Planteome Ontology Development Working Group Wiki).
There are 17 species listed with fewer than 10,000 annotations. Who maintains/adds these, and how can I?
Is Brandon able to receive training that was provided at the November 2015 curator training workshop?
Are we able to link PO terms to the Virtual Plant website?

Generic germplasm annotation script now has options and documentation.
- Newest version is up on Planteome/common-files-for-ref-ontologies/scripts/germplasm_annotation
- Included in the folder is the python script: planteome_germplasm_GAF_translation.py
  - Sample original data sheet in both .csv, and .tsv
  - Sample trait map in .csv format

3K rice genome germplasm from OryzaSNP.org is now loaded.
- DBXref has been updated, and links to specific germplasm pages on OryzaSNP are now functioning (Thanks Loc!).

Still questions:
- Column 16 display: currently including trait name. Eg: has_phenotype_score(Basal_leafsheath_color_at_vegetative=60)
- Many traits from the entire GRIMS collection have both a score and "description"- which to annotate (both)?

BS is attending
most technically sophisticated ontology meeting, non computational
what relations should we use, how are ontologies taught?, what an object is?
High level ontology design and engineering
Planteome could present results in 2018, when we have some results - held every two years

Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
- Short papers, up to 4 pages (will be published in JBMS)
- Poster abstracts, up to 1 page
- Flash updates, up to 1 page

@@ Line 35: / Line 35: @@
-=Update from Annotations from IRRI=
+==Update from Germplasm Annotations==
+* Generic germplasm annotation script now has options and documentation.
+** Newest version is up on Planteome/common-files-for-ref-ontologies/scripts/germplasm_annotation
+** Included in the folder is the python script: planteome_germplasm_GAF_translation.py
+*** Sample original data sheet in both .csv, and .tsv
+*** Sample trait map in .csv format
+* 3K rice genome germplasm from OryzaSNP.org is now loaded.
+** DBXref has been updated, and links to specific germplasm pages on OryzaSNP are now functioning (Thanks Loc!).
+* Still questions:
+** Column 16 display: currently including trait name. Eg: has_phenotype_score(Basal_leafsheath_color_at_vegetative=60)
+** Many traits from the entire GRIMS collection have both a score and "description"- which to annotate (both)?
 = Upcoming Meetings and Workshops=