Plant Ontology Webinar- May 2011 release

POC meeting with Physcomitrella group, Webex Conference Call; Date: Tuesday Tuesday June 21st, 2011 7am PDT/10 am EDT/4pm Germany

In attendance: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Marie Alejandra Gandolfo (Cornell University), Dennis Stevenson (NYBG), Justin Preece (OSU)

Absent: Barry Smith (University at Buffalo, NY), Chris Mungall (Lawrence Berkeley National Lab), Justin Elsner (OSU)

Collaborators: Stefan Rensing and Daniel Lang (absent) of the Physcomitrella group, University of Freiburg, Germany Cosmoss Moss Ontology, along with their associates Manuel Hiss and Peter Szovenyi

Expertise: Physcomitrella genomics, Moss Ontology

Link to ppt presentation: File:PO-Physco Webinar 6 21 11.pdf

Streaming recording link: [1]

Download recording link: [2]

Goals:

• To give the Physcomitrella group a brief overview of the Plant Ontology and its principles (Laurel)

• To demonstrate how to navigate the PO site, download the ontology or annotation files and request new terms, editing tools etc (Ramona)

• To demonstrate the new Plant Ontology terms and other changes that have been made to accommodate mosses (Ramona)

• To illustrate the annotations and demonstrate the utility of linking to the PO terms (Laurel)

• To encourage continued cooperation and collaboration between our groups

Organizing Principles of the PO and the Ontology Structure

Two domains: PGDSO and PAO (focus on PAO)

-Top level of PAO: plant structure, plant anatomical space, portion of plant substance

• How terms are organized within the PAO:

(1) by homology, if it is known (2) by structural, developmental or positional similarity

For example:

We group sporangia together, because there is good evidence that they are homologous across land plants.

Flowers, inflorescences and strobili are grouped together as reproductive shoot systems. We don't know the exact evolutionary transformations between the different structures, but we know that they are all shoot systems that bare sporangia.

We group vascular leaves, petals, sepals and sporophylls together. They appear to be homologous, but more importantly, they share structural and developmental characteristics (all are lateral organs that develop from an SAM). We know that vascular and non-vascular leaves are not homologous, but we group them because of their structural and developmental similarity.

The PO is a hypothesis that can change as more information becomes available.

• Aim for single inheritance, use multiple inheritance if necessary for users. If possible, have only one asserted is_a parent, other should be inferred by cross products (this will not always be possible).

Relationship types

• put in link to appropriate page...

is_a, part_of, develops_from, has_part, participates_in, adjacent_to

Genus-differentia form for definitions

-this means one needs to read the definition of the ancestor term to understand definition of a child term

• Relations are a part of the definition

• Definitions and names are taxonomy-neutral; should fit any species in which that structure occurs

-comments and subsets help clarify when a term is only used in certain taxa

Navigating the PO

Downloading the Ontology File

SVN access

requesting new terms

Sourceforge tracker

• Creating an account and logging in

• Setting preferences

• Requesting new terms

• Commenting on current trackers

Important changes that had to be made to accommodate mosses and other non-angiosperm plants

Describing the plant life cycle

• The new terms gametophyte phase (PO:0028003) and sporophyte phase (PO:0028002) were added to the PGDSO (during an earlier release).

Also added protonema phase, for bryophytes and pteridophytes. Other life cycle/growth phases will be added in future releases.

• The terms gametophyte and sporophyte were made obsolete, and added as synonyms of whole plant.

If one wants to describe a gametophyte, they should use whole plant (PO:0000003) in the gametophyte phase (PO:0028003).

• Use of the participates_in relation allows us to specify structures that only occur in one generation or the other.

For example, seta participates_in sporophyte phase, gametophore participates_in gametophyte phase.

New mid- to lower-level terms and reorganization to accommodate all plants

• Added important structures for non-angiosperms that were missing from the PO: sporangium, gametangium, protonema, gametophore, thallus, apical cell, seta

• Added new terms for structures that only occur in the gametophytic generation: antheridium, archegonium,

• Redefined mid-level terms to fit broader range of taxa (often had to obsolete and replace, if definition was very different). Example: megagametophyte, microgametophyte, microsporangium,

• Created general mid-level categories that fit all plants, with specific children for structures that differ among taxa.

Examples:

-sporangium>microsporangium>pollen sac

-apical cell>shoot apical cell>leaf apical cell>non-vascular leaf apical cell

-archesporial cell>male archesporial cell or female archesporial cell

• Added synonyms that are used for non-angiosperm plants:

Top-level classes were redefined, and new classes were added, to encompass all structures:

Theses changes were important for all plants, not just bryophytes

New upper-level classes:

• collective plant structure

• cardinal organ part

• collective organ part structure

• embryonic plant structure

• rhizoid

• trichome

• plant anatomical space

Redefined upper-level classes:

• in vitro plant structure

• plant cell

• plant organ

• portion of plant tissue

• whole plant

Organization: general terms and part_of children

Some classes that occur in both vascular and non-vascular plants (e.g. vascular leaf and non-vascular leaf) have parts that can occur in either type (e.g., leaf epidermis, leaf lamina). Creating separate part_of children for each type would lead to term inflation and an overly complex ontology structure.

Need to talk about parts of leaf, how to annotate to part, plus vascular and non-vascular leaf.

Annotations

• Searching for annotations

• Contributing annotations

4. Q&A

SR: Are there tools for creating annotations on a genome-wide scale or for large data sets?

TextSpresso- Text mining tool- need a library of gene names and symbols

-Functional annotations and expression profiling data are the logical place to start to link to the PO

-creation of mapping file has been mostly already done

-annotate library, above the level of significant expresed

-via library vs individual genes

-TAIR script runs every week, uploaded when we do a release

-contributors are responsible for their own data updates, database is populated with a "snapshot" at the time of the release.

- SR: we are currently using GO for bias and cross-species analysis would like to annotate all data sets with the new PO terms. Would like to expand to anatomy and developmental processes. So far the annotations are not being submitted to GO.

May be able to display GO functions in the PO site as well at some point in the future. Get the complete picture.

Sharing data with Gramene, as well- Gramene is hosting the Physcomitrella genome, as part of the collaboration with Plant Ensemble in Hinxton

SR: Had contacted Plant Ensemble a few years ago. Gramene tried to do annotations/predictions of Physco are not coordinated with their group- concern that there will be more than 1 version out there. Physco annotations came from JGI, not the recent version. PJ will help coordinate with the Gramene genome team and get the correct version.

SR: The NCBI, JGI- Phytozome and Plaza Database(Ghent) have all agreed to use the same versions (currently 1.2) and regular synchronization. Not a good idea to have other versions around. Phytozome currently shows version 1.2.

MH: Can you make links to gene expression data on GeneVestigator? We are in touch with as GV as they use our terms.

Physcomitrella is currently been incorporated in Genevestigator, so maybe the easiest thing to get the expression data into PO would to cross connect with them? Problem is that it is proprietory database. Need to get the PO updated at GV. PJ will contact them and see if we can get the terms updated.

Gramene is collaborating with EBI Atlas project- ArrayExpress- Expression libraries and open source. Could be mirrored here. Us the webservices to display the expression data on the genome.

5. Outreach

-Encourage Physco group to reach out to moss community to let people know about the PO.

-Encourage bryophyte researchers to contribute annotations to PO