Planteome Release 2.0 February 2017

 Notes for Planteome Release 2.0 February 2017

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Changes to the Plant Ontology:

 

Addition of fruit types:

This new release includes the addition of 21 subclasses of fruit (PO:0009001). The addition of these fruit subclasses increases the granularity of fruit and will increase the resolution and biological relevance of annotations. These new fruit types have been delimited with respect to the state of pericarp layers, seed attachment, dehiscence, and in some cases receptacle tissue, at fruit maturity. Additionally, a multitude of obsolete, traditional, and recent synonyms have been added to each fruit type, as well as synonyms in Spanish and German. Comments have been added to each term to educate the user, as well as to guide annotation choice.

 

 

Other new terms:

  • ear infructescence axis (PO:0025623) #655
  • carpel abaxial epidermis (PO:0025617) #639
  • carpel adaxial epidermis (PO:0025618)  #639
  • lateral root spine (PO:0030088) #632
  • shoot-borne root spine (PO:0030089) #632
  • root periderm scar (PO:0030090) #635
  • silk (PO:0006488) (new-ish)  #376

Revised terms:

  • style (PO:0009074) #376

  • mericarp (PO:0020075) #654

  • juice sac tissue (PO:0006013) #657

  • pneumatophore (PO:0025357) #653

  • tassel inflorescence and related terms #537

  • lenticel (PO:0000031) #633

  • plant organ margin (and related) terms #72

  • leaf sheath (PO:0020104)  #661

  • plant ovary related terms - #280

  • stigma (PO:0009073)

 

Other Changes:

  • Added synonym scopes so they show up

 

PO: Added taxon ids for some terms:

  • Now importing a slice of the NCBI taxonomy

whole plant PO:0000003

relationship: only_in_taxon NCBITaxon:33090 Viridiplantae {source="cjm"}

 

plant ovary PO:0009072

relationship: only_in_taxon NCBITaxon:3398 Magnoliophyta {source="GO:0035670"}

 

Changes to Plant Trait Ontology

  • Revised def'ns for alpha-amylase activity trait (TO:0000288) and beta-amylase activity trait (TO:0000338), so they are actually traits and include the genus.

  • Updated equivalence axioms for alpha-amylase activity trait (TO:0000288) and beta-amylase activity trait (TO:0000338)

  • Added relationships: has_relative_phenotype and has_absolute_phenotype for IRRI rice germplasm

  • Few other minor edits, but have not implemented the major changes in the DP branch

Four new crop-specific trait dictionaries mapped to TO:

  • Soybean traits

  • Pigeonpea

  • Maize

  • Sweet potato

 

New Annotation Datasets:

* IRRI GRIMS (Genetic Resources information Management System)

~130,000 accessions from the International Rice Research Institute's germplasm collection.

48 Trait Ontology traits annotated.

IRRI traits were mapped to Trait Ontology terms by Jeffrey Detras of IRRI, and manually verified by Planteome curator, Austin Meier.

These annotations were generated using the IRRI trait map, and an automated python script.  GAF annotation files were grouped using the first letter of each IRRI trait to make files more manageable.

 

* GRIN Global - maize and wheat~15,000 maize accessions

22 maize traits

~32,800 wheat accessions

22 wheat traits

- The Samara webscraping platform written by Jorrit Poelen was used to gather germplasm data from all species housed on USDA's GRIN Global resource.  The tabular file was filtered to extract all maize and wheat accessions.  

- GRIN descriptors for these files were mapped to the Plant Trait Ontology, and using this map file, and a python script, GAF annotation files were produced.  

Separate files for each crop were uploaded to the SVN.

 

 

Number of annotations and bioentities:

Total number of annotations

21,206,117

Total number of unique bioentities (genes, germplasm, QTLs, etc)

2,000,665

 

         Links to detailed annotation statisitics: