Sept 22nd, 2015- Ontology Working Group Meeting

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Agenda

Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/655429261

  • In attendance: LC, AM, EA, MAL, PJ, CM, BS

1. Ontology Development Meeting in Corvallis- November 2015

  • Discussion of Workshop scheduling and what would be covered (and other strategy meetups):

Date planning: Week 2 Nov (9th-13th)

  • Issues
  • EA - tentatively will be traveling week 2 of Nov., but will check on the dates.
  • CM - week 1 doesn't work, week 2 works.
  • PJ - week1 in Dec doesn't work.
  • BS - comes for first/second half for a few days for the strategic planning.
  • Agenda of workshop: Three parts:

1. Strategic planning (core group and PIs)

  • Coordination between the Crop Ontology and Planteome
  • Plan to have strategic discussions with the PI team to clarify the plans and details - can be on Zoom (difficult to schedule with that number of people)
    • LC will send a doodle poll to set up

2. Curator training: GitHub, Protege, TermGenie

  • Ontology development training
  • CM is fine training twice, exposure, then larger group
  • First training: week 2 of Nov.
  • Second stage 2-3 days before or after PAG
  • Who? Curators from IITA and CIP are interested- Afola and Reinhard


3. Hands on curation/annotation


4. Software team: AmiGO2

  • CM and SC could attend and work with JE in person on the AmiGO2


From the breeders group, EA, MAL:

  • Cassava file has been posted on the GitHub- from the meeting between CassavaBase and CO in Montpellier
  • Naama Menda uses the Cassava OBO file generated from Java (Marie's code), not created and edited in OE
    • Afola maintains OBO file- so where is it? Is it the same one??? The files that Afola was maintaining has been modified in order to be compliant with the notion of the variable. Now, the file on Github that Naama uploaded is the one that is maintained by Afola.
  • Both Afola, Naama and Reinhard would prefer to use the OBO file or even better, work in Protege
  • They discussed how to harmonize efforts between CO, CassavaBase and Breeding Management System- traits and variables, common semantics
  • Developed an agreed-upon process that involves MAL's script to transform the excel file to OBO
  • This addresses the needs- will start with CassavaBase, move to roots/tuber crops in the RTB program
  • new 9/10 annotation file for Cassava conversion is up
  • An OBO file will be maintained
  • Will this work? Them in OBO/excel, us in OWL.
  • Would general ontology training/OBO training help?
  • Can we convert from excel to OWL : Yes.
  • Unfortunately, the early November dates may not work for Afola and Reinhard, but may be able to join meeting at PAG
  • PAG- will be used as a second meeting/continuation of the OSU workshop
    • Continue strategy and OWL training for those who make it to OSU in Nov, and fill in people who couldn't make it.
    • PJ probably not going to PAG- or perhaps just for the weekend
    • Can use travel funding to fly curators out to PAG if they can't make OSU workshop


Please see the notes here: Planteome_Curator_workshop_Fall_2015

2. Annual report due now

  • Year 1 final report due
  • next 2 weeks (it's been due since Sept started)
  • put it on the Drive, so everyone can add their components
  • components:
    • who has been listed and working on the project
    • Time that people have spent on the project- email addresses
    • Might be asking for additions

3. Update from Bioversity:

  • Progress on mapping the CO vocabularies and creating cross products

On going results are in repo ibp-crossproducts: https://github.com/Planteome/ibp-crossproducts

The formal definitions are based on BFO.

Review of existing ontologies (trait, phenotype, ...) are described here : https://github.com/Planteome/ibp-crossproducts/wiki/Related-work

Formal definitions by trait types are described here: https://github.com/Planteome/ibp-crossproducts/wiki/Rules-used-to-build-formal-defintions

Plant Trait definition (what I understand of what is a trait): A plant trait is a quality of Process or a quality of a plant Entity.

Plant Trait definition (Manchester syntax): supposed to be the translation of the above definition (what do you think?) 

  Quality and s_depends_on some (Process or (Plant Entity or part_of some Plant Entity))

Intersection of a quality and either a Process or a Plant Entity.

Stat: about 25% of the traits that are in TD version 5 (9 crops) are currently defined with a formal definition. I based this work on the content if the columns 'Entity' and 'Attribute' of the TD version 5.

Question: Traits are classified under PATO Quality, e.g. Seed Color in under PATO color. Does this sound good?

Note: I didn't find the URIs of the BFO properties (MAL)

Examples

Seed Color 

  color and ('inheres in' some seed)

Intersection of Color (specifically dependent continuant) and a specifically dependent continuant (indeed, the domain of inheres_in is specifically dependent continuant) that exists only if seed exists.

Aluminium Tolerance 

  'tolerant to' and ('inheres in' some ('aluminum nutrient regimen' and 'whole plant'))

Intersection of Tolerant to and a specifically dependent continuant that depends on both the presence of a plant and an aluminum nutrient regimen

Amylose content (of the tuberous root) 

  composition and ('inheres in' some (amylose and ('continuant part of' some 'tuberous root')))

Intersection of Composition and a specifically dependent continuant that exists only if ( the intersection of amylose and a continuant (which is a part of a tuberous root) )exists.

Flowering Time 

  time and ('s depends on' some (flowering and ('has participant' some 'flowering stage')))

Intersection of Time and a specifically dependent continuant that exists only if the intersection of (the Process Flowering and A Process that exists only the Flowering stage exists) exists

From OBA:

Plant trait: 

  'biological attribute' and ('occurs in' some 'whole plant') and ('has quality' some quality)

Intersection of a biological attribute and a process (domain of occurs in a process) and an independent continuant (I assume that the domain of has quality is an independent continuant)

seed color 

  'biological attribute' and ('has quality' some color) and ('attribute of' some 'seed coat')

Intersection of an Biological Attribute and an independent continuant (I assume that the domain of has quality is an independent continuant, so something that have a color) and something that have an attribute (attribute of is not described, and I am not able to guess the domain of the property)

4. ICBO Meeting, 2016, Corvallis

  • Need to create a web page and send out a notice
  • ICBO conference
  • JE will set up a site - ICBO-2016-conference.com
    • might need to host on our stuff, can be complicated.
    • a portal exists ICBO-conference.org
    • can link to that domain name ^
  • BS will work with PJ on the details for the committee
    • Get the announcement out as soon as possible, so people have plenty of warning
  • OBO started as Open Biological Ontologies, and now it's "Biomedical"
    • need to make it clear we are not making biomedical assumptions
    • change the name to just use 'Biological'
    • already a CSO (chief science officer) lined up as potential headline speaker
    • USDA chief science officer also an option

Next meeting: Sept_29th,_2015_Ontology_Working_Group_Meeting

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