June 14th, 2016 Ontology Working Group Meeting

Planteome Ontology WG Zoom Meeting

• Date: Tuesday June 14th, 2016
• Time: 8:15am PDT (GMT-7)

• Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/132105144
• Attendees: LC, AM, PJ, JE, EA, MAL, DWS, BtSinn, Dario, CJM, Luke, GG
• Regrets: BS

Recordings:

• File:Ontology WG meeting 6-14-16 video.mp4
• File:Ontology WG meeting 6-14-16 audio only.m4a

1. Update from NYBG: Welcome Brandon Sinn to the project

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.
  • 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

• File storage for images: Currently saved on NYBG servers, PJ suggested to use DropBox for sharing
• Bsinn and DWS will work with JP and the Bisque team to do the image annotations etc

• 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?

- Yes, we will probably have another meeting this fall

• Are we able to link PO terms to the Virtual Plant website?

This is the website for DWS' Plant Anatomy textbook site. Linking to this should not be a problem

Meeting notes: Dennis' imaging:

 - his group is imaging everything they can, getting images on all important terms
   - root and shoot anatomy.
   - images, or slides
   - link back to Dennis' anatomy book
   - in situ and link back to GO terms
   - include arabidopsis, medicago, brachipodium, populus, musa, maize or rice.
   - storage:
     - Dropbox: backed up online and shared with the whole group.  Keep pictures here.
 - moving to do some fern stuff to get ahead of the EvoDevo guys.
   - Dennis is collaborating with some people doing whole fern genomes
 - lean towards increased machine learning.
 - the virtual plant website.
   - http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/

- Brandon's intro:

 - he would like to help with "Orphan genomes"
   - many of these orphan genomes get created, and then left to gather dust.  No frequent updates.
   - transcriptomes often discover novel genes that are not present in the published genomes.
   - 1KP - Dennis is a co-PI on this.  So the resources 1400 transcriptomes will be available to the public once the keystone papers get out there.
     - 1KP website
       "https://sites.google.com/a/ualberta.ca/onekp/"
 - looking to gain more experience on comparative genomics, and whole genome annotation.

2. Update from Bioversity- Crop Ontology

MAL: newest trait dictionaries being completed:

• wheat - in progress; MAL is doing the mapping

- Rosemary validated the mappings during the Montpellier workshop - MAL will create the OBO file after it is checked over, will add common name in the trait names

• maize - trait dictionary not finished

- PJ: most of the maize trait terms in the Trait Ontology (???)

• Sweet Potato Ontology (or TD?) has been released

• Rice:

- list of traits has been validated - more traits are being added by CIAT and African Rice project - adding some pathology traits

• Goal is to complete as many of them by the end of June

3. AmiGO updates

• JE: - update on AmiGO release

- close to a non-beta release of the new AmiGO - multiple annotations coming from different sources, causing redundancies in annotations in GO datasets - Can we find a mechanism to concatenate them together?

• Possibly will be able to filter out redundant annotations in future AmiGO release, but for now, it will have to be done before loading them.

• Need to finish cleaning up the object types
• Still some issues with the drill down browser.... see tracker https://github.com/Planteome/amigo/issues/16

4. Update on Germplasm Annotations and PDO

• 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)?

• Update on contractor- Yorick

- APS plant net scraping - Yorick (EOL) - will focus on the crops that we have not done - capturing host and pathogen taxa - works with EOL

• AM is looking at a "design pattern" for the PDO

- CJM: Are you familiar with YAML- tutorial from workshop, dont use ONTORAT, CM will send the info

• Future work for Yorick: Plan is go to GRIN, to get the list of traits, germplasm repositories for all of the US

- nursery trials- etc; everything in there has some description of phenotypes - they use their own vocabularies, so Yorick can put these into ontologies so we can automate the annotation of these GRIN stuff.

5. Reverse Site Visit with NSF- this fall

• Comments from PJ:

- Our project has been assigned to new project manager- not Diane any more - Should have some concrete results by ~ Sept - Advisory Board meeting will be set up in the fall- show our progress - If site visit goes well, should get third year funding and possibly forth

-Need to move into HTP phenotyping traits- data and annotations

Update from Birmingham

• Luke's update:

- Working on adding a semantic querying functionality to Agroportal using AberOwl - Will be attending ICBO, along with Mona and Migel from Robert's group - LC will send an email to group about having a project meeting on Aug 5th and 6th

• George's update

- looking to get all the HTP phenotyping data from European groups - We would like to get a workshop specific to HTPP to get ahead of the data that is being generated, maybe this fall/winter - GG want's names of groups doing HTPP in US - INRA - has reverse-engineered Lemnatech's system, and is selling their reverse engineered system - Lemnatech - Australia

List of US HTP Phenotyping Centers:

• Bellwether Foundation Phenotyping Facility at the Donald Danforth Plant Science Center

Planning for ICBO/BioCreative Conference

• Link to program: ICBO + BioCreative

Meeting notes: - Dennis' keynote

 - why do we have the ontology?
 - where might ontology go?
 - comparative/phylogenomics
 - finding convergent evolution of structures - if different plants form similar structures independently, that might be of interest to geneticists, and breeders.
 - connecting GO with PO

- ICBO coincides with the botanical society association

• Link to workshop page: Plant Biodiversity Workshop
  • Title: Tools and Applications for Data Standards and Knowledge Sharing in Plant Biodiversity
  • Workshop type: Project Workshop (Project specific talks + Discussions)
  • Organizer: Laurel Cooper, Oregon State University
  • Co-organizer(s): Dennis Wm. Stevenson, Chelsea Specht, Marie-Angelique LaPorte

Upcoming Meetings and Workshops

9th International Conference on Formal Ontology in Information Systems (FOIS 2016), Annecy, France on July 6th-9th, 2016

• http://www.iaoa.org/fois2016/

• 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

BioOntologies SIG of the Intelligent Systems for Molecular Biology (ISMB); July 8-12, 2016, Orlando, Florida

• 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

7th International Conference on Biological Ontology and BioCreative 2016 Aug 1st to 4th, Corvallis, OR

• Link to program: ICBO + BioCreative Program
• Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589