Sept 15th, 2015- Ontology Working Group Meeting

Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)

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

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

• Link to recording- Video: File:Ontology WG 9-15-15.mp4
• Link to recording- Audio: File:Ontology WG 9-15-15 audio.m4a

Agenda

1. Upcoming Plant Ontology Release #21

- Many changes and updates to the PO which will accompany the PSDS paper submission

• Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
• PO Live Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN-
• Timeline- within the next 2 weeks
• For more information: Plant_Ontology_Release_#21

• New association data developed from the [1] paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
  • Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations

• New association data developed from MaizeGDB (Mary Schaeffer)
• Based on data set from Scott Stelpfulg et al (Kaeppler group): "An expanded maize gene expression atlas based on RNA-sequencing and its use to explore root development"
  • The Plant Genome doi:10.3835/plantgenome2015.04.0025
  • Accepted paper, posted 08/07/2015.
  • Update of the Nimblegen Microarray data - more tissues, not so much background noise

2. Planteome.org Update:

• Once the Plant Ontology update is pushed out, we will be rolling all the data files and updated ontologies to the Planteome web page: Planteome.org for our Planteome 1.0 release.
• This is important as we are getting ready to submit our first annual report and people are using the Planteome site, so we want to make sure it is all working well.
• We are diligently working to make sure all the dbxrefs and links are updated, so if you find any issues, please let us know.

3. Plant Trait Ontology:

Questions from Barry about how to define the traits:

Anatomy and Morphology traits

> Are there any traits which are not anatomy and morphology traits?

There are 8 different branches in the TO, anatomy and morphology trait is just one.

* Note that there is a still a class "other miscellaneous traits" which we are planning to get rid of soon.

> Is there a definition of 'anatomy trait' and of 'morphology trait'?

• LC: My understanding of the meaning of anatomy and morphology in botany are as follows: the anatomy is the internal structure and the morphology is the external structure. This is consistent with the definitions of plant anatomy and morphology in common use:

• plant anatomy: "The general term for the study of the internal structure of plants. While originally it included plant morphology, which is the description of the physical form and external structure of plants, since the mid-20th century the investigations of plant anatomy are considered a separate, distinct field, and plant anatomy refers to just the internal plant structures.[1][2] Plant anatomy is now frequently investigated at the cellular level, and often involves the sectioning of tissues and microscopy.[3] (from : https://en.wikipedia.org/wiki/Plant_anatomy)

• Plant morphology: "The study of the physical form and external structure of plants.[1] This is usually considered distinct from plant anatomy,[1] which is the study of the internal structure of plants, especially at the microscopic level.[2] Plant morphology is useful in the visual identification of plants." (from https://en.wikipedia.org/wiki/Plant_morphology)

• Current def'n: anatomy and morphology trait (TO:0000017): A plant trait (TO:0000387) which is associated with the anatomy or morphology of a plant anatomical entity (PO:0025131) or one or more constituent cellular components (GO:0005575) contained therein.
  • Comment: Includes traits of plant structures (PO:0009011) such as plant cell (PO:0009002), plant organ (PO:0009008), portion of plant tissue (PO:0009007), vascular system (PO:0000034), whole plant (PO:0000003) and seed (PO:0009010), as well as those of plant anatomical spaces (PO:0025117) and portions of plant substance (PO:0025161).

> Are they logically disjoint?

• Based on the definitions above, they are logically disjoint

> The term 'anatomy and morphology trait' really means 'anatomy trait or morphology trait', right?

• The class is designed to be inclusive- covering physical traits that are either internal (anatomy) or external (morphology), so 'anatomy trait or morphology trait' would perhaps be more correct.
• If we say "anatomy and morphology trait", does that mean that the trait in question is both an anatomical and a morphological trait?

Test classification of some of the subclasses of PSA+M traits as either anatomy or morphology traits:

Examples of morphological trait classes

• awn length, width, thickness, color, presence (?)
• leaf margin serrated
• seedling hypocotyl size
• axillary bud shape
• plant cell shape, size, length
• embryo shape, shootless embryo
• flower or floret color, type, diameter, length, number, shape, etc
• chasmogamous flower, cleistogamus flower
• ear (infructescence) circumference, aspect, color, length, weight, position shape, diameter, circumference
• inflorescence (incl. panicle, spikelet, tassel) size, width, branching, color, density, depth, diameter, exsertion, number, presence, shape, texture, type, waxiness, weight, etc
• axillary bud number, shape, size, prominence
• leaf attitude, color, weight, cover, volume, flexibility, height, number, pubescence, adherence, shape, size, rolling, phyllotaxy, area, nitrogen content, pigment content, gloss, drying, stomatal frequency, temperature, necrosis,
• leaf lamina area, color, length, splitting, width, pubescence, joint bending, etc

Examples of anatomy trait classes:

• leaf vein color, size
• leaf midvein thickness

• Question: Would either of these classes include traits such as fruit color or leaf color? This is more a quality or atribute than an anatomical or morphological trait.

Objection to using: 'associated with'

> BS: (a) it is vague (b) it will block reasoning I agree that it is vague and would prefer a more precise statement, although textual definition will not block reasoning.

Example anatomy and morphology trait classes:

• stem number (TO:0000953): A shoot system anatomy and morphology trait (TO:0000077) which is associated with the number of stems (PO:0009047).
  • Added Xrefs to: number (PATO:0001555); TO_GIT:157

• stem size (TO:0000954):A stem anatomy and morphology trait (TO:0000361) which is associated with the size of a stem (PO:0009047).
  • Added Xrefs to: size (PATO:0000117); TO_GIT:157
  • Added narrow synonym: stalk size

Suggestions:

• "stem number =def. a trait of a plant which is the number of stems of the plant"

and so on for the other cases

• "infructescence axis shape: An infructescence axis anatomy and morphology trait (TO:0000921) that describes the shape of the infructescence axis" [or specify the 'of' further]

synonym: cob shape

Examples from other from OBO_Foundry_Ontologies that concern traits:

Vertebrate Trait Ontology: http://www.berkeleybop.org/ontologies/vt.owl -- “related to”

Animal Trait Ontology: http://147.99.159.184:8080/webprotege/#ATOL -- “related to”

• name: has_quality (id: RO:0000086)
• def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence"

property_value: IAO:0000112 "this apple has quality this red color" xsd:string property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "has_quality" xsd:string

Possible solution using relations from RO:

ear shape (TO:0000964): An infructescence anatomy or morphology trait (TO:0000920) an ear infructescence (PO:0025597) has_quality shape.

Added dXrefs: shape (PATO:0000052);

Example from BATTO: http://www.ontobee.org/browser/index.php?o=oba

[Term] id: TO:0000431 ! ear length intersection_of: BATTO:0000001 ! biological attribute intersection_of: affects_quality PATO:0000122 ! length intersection_of: attribute_of PO:0020136 ! ear (sensu Zea)

4. 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

Trait definition (Manchester syntax):

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

5. Proposed: Ontology Development Meeting in Corvallis early November-

Please see the notes here: Planteome_Curator_workshop_Fall_2015

5. TermGenie Demo

• A tool for creating new ontology terms for either GO (Gene Ontology) or OBA (Ontology of Biological Attributes). It uses a pattern-based approach to rapidly generate new terms and place them appropriately within the ontology structure. All terms are reviewed by a senior editor before the final commit to the ontology.

• Two instances of TermGenie exist: for OBA and GO:
  • TermGenie GO

• • TermGenie OBO

• Citation: TermGenie - a web-application for pattern-based ontology class generation

Discussion of TermGenie tabled for next meeting"