Ontology Working Group Meetings- Feb 2015

Tuesday, Feb 10th, 2015

Who: PJ, EA, LC, JE, CM, BS

• Meetings will be held using Zoom (https://www.zoom.us/) - we are in the process of getting it set up
• Wiki is set up and notes will be kept here, need to login to access

1. Coordination between the species-specific Crop Ontologies and the reference ontologies- PO, TO, GO etc

PJ: Initial goal will be to work on improving and updating the TO

EA provided an overview of the Crop Ontology curation tool (http://www.cropontology.org/) and some background information about the ontologies and platform.

Long term goal is to integrate the CO vocabularies with the reference ontologies.

• Part of the Integrated Breeding Platform
• Common vocabularies are used to integrate data from breeders field book
• Was started as part of the Generation Challenge Program (GCP), which has run out of funding. The GCP Pantheon webiste (http://pantheon.generationcp.org/index.php) will be shut down soon and so that information needs to be moved somewhere else. Could perhaps go the the GCP Wiki page?

• 18 crops (http://www.cropontology.org/) represented in five sections:
  • General Germplasm Ontology
  • Phenotype and Trait Ontology
  • Structural and Functional Genomic Ontology
  • Location and Environmental Ontology
  • Plant Anatomy & Development Ontology

Cassava Example: http://www.cropontology.org/ontology/CO_334/Cassava

• Based on OBO-Edit
• Excel-based template
• Visualized by the tool

Common Trait Classes (e.g.) : Maize Ontology (http://www.cropontology.org/ontology/CO_322/Maize)

• "Agronomic/Agronomical"
• Morphological
• Stress (Abiotic/Biotic Stresses)
• Phenological
• Quality
• Unit

Relations:

• is_a
• part _of
• method_of
• scale _of
• derived_from

Availability and Formats:

• Download from www.cropontology.org
• API- http://www.cropontology.org/api
• make 'Permalink' to individual terms pages
• Formats include csv, OBO, SKOS, RDF, Trait Template v4
• Ones in blue are OBO based
• Terms are translated into various languages, as synonyms

Terms have a unique identifier:

• CO_###:#######

Questions and Discussion:

• Goal is to keep the web-based tool for user access, in some form.
• Database behind it is No-SQL based
• Integration with future versions of Term Genie
• We will need a technical call as we we move towards integration at GitHub
• The Trait Ontology is not displayed here as it was confusing to the users.
• Identified an issue where curators/users can upload an ontology without any quality control.

2. Prioritizing the work on the species-specific Crop Ontologies- Rice, Wheat and Maize

• At the PAG meeting- Rice, wheat and Maize were identified as the best candidates to start on
• The PO is well set up to provide entity terms for these as they are important crop/model species
• The TO has some of the needed terms, but will need additional work

Fill in some details of the Rice, Wheat and Maize vocabs here:

3. Transition to GitHub Repository

Planteome Ontologies on GitHub

• This will be very useful for editting and versioning, then the relased version can be pushed out to Crop Ontology site

4. Hiring at Bioversity, OSU and NYBG

• Bioversity Curator position is advertised on the Bioversity Jobs page:

You can view it here: Position Description: Post Doctoral Fellow, Crop Ontology, MPL

• Ontology Curator Position at OSU: In progress....

• Ontology Curator Position at NYBG: In progress....

5. Possible Ontology development workshop this spring

Time is quite short, maybe consider a web-conferencing strategy to start, new people are being added to project at OSU, NYBG, CO

6. White paper on plant phenotyping standards

See details on All Hands Call Feb 6th

Tuesday, Feb 17th, 2015

Who: PJ, LC, CM,

1. Discussion of the GitHub Repository: https://github.com/Planteome

• Intro to the GitHub- site for the Planteome
  • Procedure will be to do a check out. Two-step commit process: make changes and then commit locally, then do a "push" to synchronize with the server version.
  • Branching: It is different than forking

• What is 'Forking': (we probably won't need to be doing this)
  • You can copy a version of the ontology into your own user space to make local changes, changes can be made there, and then a make a "pull request"
  • Administrator can review the pull request and look at the difs, and select the parts that are accepted. Can also be voted on by the project members
  • Works best if the files are easily "diffable", OBO works well, OWL not so well suited for this. Possible changes coming to OWL to make this work better.
  • Different than doing a check out

2. Overview and update on the Plant Trait Ontology

- The Trait Ontology can be accessed in various ways:

• TO-Dev AmiGO Browser
• TO-Dev on Planteome Browser
• Link to TO on SVN

Updates on the Trait Ontology:

• Early work (~2005-2011) on the TO was done by PJ and CWT at Gramene, primarily to describe QTLs of rice
• Since 2012, the Trait Ontology has not been funded under the PO grant
• Large amount of interest from the community drove the TO forward Crop Plant Trait Ontology Workshop OSU 2012
• A significant amount of work has been done to make the TO compatible with the PO and other reference ontologies
• In Summary:
  • Revised def'n of the root term: plant trait
  • Many changes to eight top level classes, new terms added, revised names of others
  • Renamed and added new upper level terms to align the anatomy and morphology trait (TO:0000017) class with the plant anatomical entity (PO:0025131) branch of the PO
  • Many new child terms added
  • Definitions revised to contain references to the entity term (from PO or GO) and quality term from PATO
  • Xrefs added to SF trackers
  • Full details of the changes have been documented on the Trait Ontology Wiki page and the Trait Ontology SourceForge tracker
• Changes are currently stored on the SVN, with notes as to the nature of the changes.
• A version of the TO was branched or forked out to GitHub in April 2014 (https://github.com/Planteome/plant-trait-ontology) and a large number (~680) of new terms from the TRY database were dumped in the ontology. This version is now out of sync with the main version.

Logical Definitions; i.e. Cross Products

• Chris has done some work on setting up logical definitions (also called Cross Products)
  • Cross products are a way to 'decompose' the TO terms into the element entities (from PO, GO, ChEBI or other ontology) and qualities (from PATO).
  • This allows automatic classification by the reasoner - so the computer can make inferences across the ontology
  • Cross product file is currently stored on our SVN: trait_xp.obo last updated 16 months ago

• Example: ligule length (TO:0000024)

id: TO:0000024 ! ligule length

intersection_of: BATTO:0000001 ! biological attribute

intersection_of: affects_quality PATO:0000122 ! length

intersection_of: attribute_of PO:0020105 ! ligule

• ligule- PO:0020105 (is_a cardinal organ part; part_of vascular leaf)
• length- quality from PATO
• BATTO- now called "OBA"- Ontology of Biological Attributes, larger ontology which unifies trait ontologies across all types of life.

In the upcoming versions of the AmiGO2, it is anticipated that we will be able to create actual relationships between the TO terms and the component entities (from PO, GO, ChEBI or other ontology) and qualities (from PATO). Thus the existing references will be redundant.

3. Panzea Project: Curating Maize Diversity with MaizeGDB

• Recent work with Mary Schaeffer of MaizeGDB which was presented at the Plant and Animal Genome Conference in January 2015.
• Link to Abstract
• Link to presentation on Google Docs: Curating Maize Diversity]
• Panzea project ([1]) at Cornell lead by Edward Buckler ([2])- breeder data for a large number of GWAS and QTL studies.
• Collaborative process of curating a set of data from 8 published papers (see list: References for the Panzea Project Annotations

• Panzea data is stored in free text a large relational data base, in the GDPDM schema, (GDPDM Home Page)

Traits are not linked to ontology terms but are based on the community's name for them; for example:

Trait	no. Locations	Trait Protocol
20KernelWeight	7	weight of 20 kernels
AGPase	1	ADP-Glc pyrophosphorylase (EC 2.7.7.27)
AlaAT	1	Ala aminotransferase (EC 2.6.1.2)
CobDiameter	8	diameter of cob at halfway point of length, no kernels
CobWeight	8	mass of cob only, no kernels
CS	1	citrate synthase (EC 2.3.3.1)
DaystoSilk	10	Days from planting date to silking date (cb)
DaysToTassel	10	Days from planting date to tasseling date (ca)
EarDiameter	8	diameter of ear at 1/5 length point with kernels on it or the widest point
EarHeight	11	distance from soil surface to the highest ear-bearing node
EarLength	8	length of cob from base to tip
EarRankNumber	7	number of rows along length
EarRowNumber	8	number of rows around circumference
EarWeight	8	mass of cob + kernels
GDDAnthesis-SilkingInterval	11	NULL
GDDDaystoSilk	10	NULL
GDDDaystoTassel	7	NULL

• Eighty TO traits have been revised or new ones added to annotate 300,000 lines in the MaizeGDB database with the ontology terms
• Germplasm includes mapping panels (200 IBM and 5000 NAM recombinant inbred) and public inbred lines, such as the Goodman diversity panel (~302 inbreds).
• Metadata about the assays are recorded in the spreadsheets
• Eventually will be able to search the MaizGDB interface using the ontology terms- TO, PO, PATO, CO etc.

CM: Recommend a more precise prefix to be used for the Crop Ontologies- such as CGIAR_CO, in order to add it to the central registry of OBO ontologies. May want to use the Assay ontology, combined with the Unit ontologies.

Plan is to eventually host these annotations at the Planteome to do more advanced searches, at least at the population level with associations with links to MaizeGDB where the bulk of the data will be stored. With QTLs and linkage disequilibrium

Tuesday, Feb 24th, 2015

Who: PJ, EA, LC, BS, DWS