The Plant Ontology A Resource for Plant Genomics

www.plantontology.org

Plant  Ontology  Consor.um  Members  and  Curators*:    

Laurel  D.  Cooper*,  Jus.n  Elser,  Jus.n  Preece  and  Pankaj  Jaiswal*:        Department  of  Botany  and  Plant  Pathology,  Oregon  State  University,  Corvallis,  OR  

Ramona  L.  Walls*  and  Dennis  W.  Stevenson:  The  New  York  Botanical  Garden,  Bronx,  NY  

Maria  A.  Gandolfo:  Department  of  Plant  Biology,  Cornell  University,  Ithaca,  NY    

Ontology  Consultants:  Chris  Mungall:    Gene  Ontology,  Lawrence  Berkeley  NaFonal  Lab,  Berkeley,  CA  Barry  Smith:    OBO  Foundry,  Department  of  Philosophy,  University  at  Buffalo,  NY  

Vision  and  Goals  of  the  Plant  Ontology:  

•  Encompass  all  plants  :  including  gymnosperms,  lycopods,  ferns  and  bryophytes  

•  Facilitate  compara.ve  genomics  across  taxa  by  linking    descripFons  to  genomics  datasets  

•  Create  mappings  (links)  to  other  ontologies  such  as  the  Gene  Ontology,  CARO  and  PATO  

•  Follow  OBO  Foundry  principles:  openness,  format,  delimited  content,  collaboraFve,  etc  

 

Challenges in expanding the Plant Ontology to covers all plants:

Bowman et al, Cell, 2007

•  Seed  plants:  Angiosperms  and  gymnosperms  

•  Pteridophytes:  Ferns  and  Lycopods  

•  Bryophytes:  Mosses,  Hornworts  and  Liverworts  

•  Algae

Complete genome sequences for 30 plant

species from Phytozome 8.0

Diversity in anatomy, morphology, life cycles, growth patterns

Phylogene.c  diversity  can  result  in  inconsistency  in  nomenclature:  

Instances of leaf: (PO:0025034)

maple leaf palm frond pine needle

Different names are used for the same structure

The PO provides consistent terminology for annotation of plant structures and growth and

developmental stages across taxa

Different structures can have the same name e.g. ‘floret’

Asteraceae Poaceae

Two branches or subdomains of the PO are now merged:

Plant Structure Development Stage (beta)

Plant Anatomy

Recent  changes  to  the  PO:  

…a controlled vocabulary

The Plant Ontology is…

Each term has:

•  primary name and synonyms

•  unique PO ID and url

•  definition vetted by experts, with community feedback

•  two aspects

•  terms cover the plant domain

…a tool for reasoning across large data sets

The Plant Ontology is…

Relations among terms allow for reasoning: “Find me all the genes expressed in a phyllid.”

costa PO:0030072

alar cell PO:0030057

plant  organ  

non-­‐vascular  leaf  (phyllid)  

cardinal  organ  part  

is_a is_a

costa  alar  cell  

part_of

plant  cell  

is_a

Image: Aisling T. Walsh

phyllid/non-vascular leaf PO:0025075

Rela.ons  in  the  PO  allow  for  an  accurate  expression  of  biology  

is_a and part_of are the backbone of all anatomical ontologies

has_part allows the PO to handle structural variation among taxa

develops_from describes shared developmental pathways across all taxa

reproducFve  shoot  system  

inflorescence  

flower  

part_of

infructescence  

has_part is_a

gynoecium  perianth  

shoot  system  

is_a

is_a

develops_from part_of

Reasoner: perianth is part_of flower which is_a a reproductive shoot system. So: perianth is part_of reproductive shoot system

…a database resource for plant sciences

The Plant Ontology is…

Links to associations from:

•  gene expression experiments

•  EST and QTL datasets

•  mutant phenotype screens

~2.2  million  associaFons  for  1320  PO  terms  covering  17  species  

The  Plant  Ontology  facilitates  compara.ve  plant  genomics  

MEE58? AtMEE58

AtMEE58

hydroid  xylem  element  

I I

plant  cell  

axial  cell  

fusiform  iniFal  

MEE58?

MEE58? D

I

AtMEE58

I

Cross-­‐taxa  comparisons:  

A guided  tour  of  the  Plant  Ontology-­‐  How to:

Ø  Navigate the PO website- browse or search for terms

and view relationships

Ø  Find annotations and links to more information

Ø  View and download ontology files

Ø  Request new terms or comment on terms

Ø  Access our new web services

Ø  Keep up to date with PO on social media http://analogicalplanet.com/Pages/ContentPages/Mosses/MossIndex.html

Navigating the Plant Ontology website

The toolbar is used to navigate within the website

Browse or search the PO web site for ontology terms or annotations

Use the Search/browse link

Or do a quick search from the home page

Term search

Type “endosperm”

Expanding nodes

To expand a node, Click on the [+] sign Next to the node/term

Term detail view: definition, synonyms, comments, etc.

To  view  the  term  lineage  in  a  graphical    format  click  on  the  Graphical  View  link  

Relations can be visualized in graphical view

Layout can be changed to horizontal

or colors can be changed

Relationship types

The relation type icons used in the tree

browser

Ontology Download Page:

19  

Different  versions  of  the  PO  file  can  be  downloaded  from  our  SVN  site:  

http://palea.cgrb.oregonstate.edu/viewsvn/Poc/tags/live/

RequesFng  new  term  or  commenFng  on  an  exisFng  term:  link  from  PO  home  page:  

Click “Request PO terms”

Takes you to SourceForge Tracker Page:

You must register and log in first.

After logging in, click “Add new”

Sending feedback via link from PO website

Annota.ons  allow  for  data  analysis:  

Data Image From: Wang, et al. (2010). The Plant Journal, 61.

Annotations may be created based on microarray, EST, QTL, protein, germplasm, phenotype or other data sets, or whole genome sequencing projects.

Example microarray data set with PO and GO annotations:

Contact us if you are interested in providing and maintaining annotations files for your project

PO terms corresponding to synonyms used in the study: * inflorescence (PO:0009049) ** shoot axis (PO:0025029) *** whole plant in the seedling stage (PO:0000003)

Annota.ons:  links  to  genomics  datasets  

•  May be created for: •  whole genome sequencing projects •  EST data sets •  QTL data sets •  protein data sets •  germplasm data sets •  phenotype data sets

•  Annotation files must be in the GAF1 or GAF2 format: 15 or 16 column spreadsheets, one line per association

Details  on  annota.on  file  format:  

http://plantontology.org/docs/otherdocs/assoc-file-format.html

Sample Physcomitrella annotations

• See http://plantontology.org/docs/otherdocs/assoc-file-format.html for more details

AnnotaFon  files  are  uploaded  to  our  SVN  repository:  

http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/

View the annotations associated with a term:

Clicking “view annotations” takes you to the annotations associated with a terms

Clicking on gene name provides more details on that gene

PO associations provide links to other databases: PubMed or other source

Link to original article for evidence of association

PO associations provide links to other source databases:

Link to source database: Cosmoss Gene Page

PO associations provide links to other databases: Gene Ontology

Link to Gene Ontology associations for the same locus

Searching for annotations

Searching annotations for “actin” returns 236 results Filtering results by “P. patens”

returns 1 result

Downloading  annotaFons  

Annotations for individual terms can be downloaded as RDF-XML files

Downloading annotations

Entire annotation files can be downloaded from our SVN site.

http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/associations/

Collabora.ve  development  of  the  PO:  descriptors  and  annota.ons  

Recent Examples: •  Addition of 1.5 million new associations between Zea mays

(maize) gene models and Plant Ontology terms (October 2011) •  ~80 new anatomy terms for the Physcomitrella- Moss

Computational Biology Resource

•  Added ~ 82,000 new annotations to Moss genomics data (Jan 2012)

MaizeGDB,  PLEXdb  and  the  PO  Sekhon  et  al.  2011      

 

B73  Maize  Gene  Expression  Atlas    Plant  Ontology  Use  Case    

Source: - Mary Schaeffer - USDA ARS - Curator MaizeGDB

Sekhon RS, Lin H, Childs KL, Hansey CN, Buell CR, de Leon N, Kaeppler SM (2011) Plant J 66:552-563 •  A comprehensive atlas of global transcription profiles across developmental stages and

plant organs •  NimbleGen microarray containing 80,301 probe sets to profile transcription patterns in

60 distinct tissues representing 11 major organ systems of inbred line B73

Jack Gardiner (MaizeGDB curator) Rajan Sekhon Robin Buell Sean Kaeppler

Source: Mary Schaeffer

60  maize  Fssues      seed  to  seed  

>300,000    NimbleGen  probes  B73_V1  based  gene  

models  

Sekhon et al Mar 2010 Maize Meeting

B73_v2  gene  models    

 Mar  2010  released  

Jack Gardiner (MaizeGDB curator)

Source: Mary Schaeffer

PO:0006469 silk PO:0009074 style; An elongated part of a carpel or group of fused carpels between the ovary and the stigma, and through which the pollen tube grows. PO:0006354 ear floret

Used style instead of silk

Information accessible from tissue record

~1.5 million new associations between Plant Ontology terms and ~35,000 Zea mays gene models from the recent sequencing of the Maize genome (Oct 2011)

Over 80 new anatomical terms have been added for bryophytes and pteridophytes

•  All tissue and cell types from the Moss Ontology have been incorporated into PO

•  Additional terms were gathered from bryophyte reference books

Examples: amphithecium, calyptra, foot, gametophore, hydroid, leaf apical cell, protonema, thallus, tmema

New Physcomitrella annotations

Added ~ 82,000 new annotations to Moss genomics data (Jan 2012 Interim data release)

PO associations provide links to other source databases:

Link to source database: Cosmoss Gene Page

PO associations provide links to other databases: Gene Ontology

Link to Gene Ontology associations for the same locus

PO association data can be used to answer questions like:

MEE58? AtMEE58

hydroid  xylem  element  

I I

plant  cell  

•  Do water conducting cells in mosses express MEE58, a homolog of AtMEE58 (gene expressed in Arabidopsis thaliana)?

•  What other genes are expressed hydroids?

non-­‐vascular  leaf  vascular  leaf  

I I

leaf  

•  How similar are the sets of genes expressed in vascular and non-vascular leaves?

•  Are there more homologs than expected by chance?

PO  Web  Services  Plant  Ontology  terms,  synonyms,  and  definiFons  are  now  available  via  RESTful*  web  services  

*  REST:    Representa8onal  State  Transfer  (an  architecture  for  web-­‐based  data  communica8on)  †  Web  service  results  are  encoded  in  JSON,  a  lightweight  data-­‐interchange  format  

Detailed  documentaFon  for  applicaFon  developers  is  available  on  the  PO  web  site  

…and  use  the  real-­‐.me  results†  in  your  applica.on  Request  terms  by  keyword:  

Come  ‘like’  us  on  Facebook  

 *    Sign  up  for  the  PO-­‐announce  mailing  list  

Participants and Collaborators:

Cell Ontology