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DAG-Edit and the flat-file format described below are no longer in use by the Plant Ontology.

Please follow this link to read about the newer OBO flat file format.


Understanding the flat file format.

The best way to visualize the ontologies is through a browser thatrepresents the data in a hierarchical tree format. The flat file formatwas originally developed as a flexible, and extensible machine parseablerepresentation. The DAG-Editontology editor is capable of both reading and writing the flat file format.Parsers have also been written to read flat files into a variety of databasesand alternative formats. This page outlines the main features of and howto interpret flat file formatted ontologies.

I. Meta-data about the file.

Included at the top of each file are comments containing descriptive informationabout the file. Comment lines are preceded with an exclamation point (!).The comment lines generally have the following format:

!autogenerated-by:  DAG-Editversion 1.401 -Text produced by DAG-Edit that identifies the version. 
!saved-by:   Pankaj -Name of the individual who created the version
!version:    $Revision: 1.5 $  -Each version corresponds to a revision with a number assignedfrom CVS
!Disclaimer: Copyright 2003 PlantOntology Consortium -Copyright statement
!Title:     Plant Growth and Development -The title of the page.
!Date:      Wed Dec 10 14:05:08 EST 2003 -The date when the file was committed to the CVS

II. Flat file format conventions: Ontology file

The following section describes the formatting used in the ontology flatfiles and their meanings.

A. Root terms

1. Each ontology starts with the root term and children terms are listedbelow their parents. The indentations represent the depth from the parentterm.The root term is designated with a dollar symbol ($).

B. Types of relationships between terms.

Relationship types are indicated using symbols preceding each term. Thisrepresents the relationship between a child term and its parent term (termto term relationship).

1. Relationship type: IS A

A percent (%) symbol indicates that term "a" IS AN instance (term toterm relationship ISA) with that of its parent term placed higher in thetree.
For example, sepal IS A type of floral organ.

 %floral organ
  %sepal
 2. Relationship type: PART OF

A less-than (<) sign is used for terms that are a part of (term toterm relationship PART OF) a parent term placed higher in the tree.
For example: sepal is a PART OF a flower.

%flower
 <sepal
3. Relationship type: DEVELOPS FROM

A tilde (~) sign is used for terms that develop from (term to term relationshipDEVELOPS FROM) its parent term.
For example: trichome DEVELOPS FROM a trichoblast.

<sepal
 <epidermis
  <trichoblast
   ~trichome

C. Inheritance and other features of terms.

Each row represents a single term. All of the information about that term(with the exception of the definition) is contained in each row includingparentage, relationship types, term identifiers and term synonyms.

1. Inheritance.

In the following example the hyphen sign (-) is used to show the indentationfrom left. In the flat files, the hyphens (INDENTS) are one or more blankspaces. Finer, more granular level terms lies at the bottom of tree andparent terms are at the top of the tree. Deeper, granular terms are indentedto a greater depth than their parent (general) terms.

For example: sepal (unique identifier=PO:0000012) is a part of a flowerwhich is a type of an organ which is a part of the plant structure ontology.

$Plant structure ontology; PO:0000001
-<organ ; PO:0000006
--%flower ; PO:0000007
---<sepal ; PO:0000012
2. Multiple parentage

It is represented with the following syntax FOR EACH LOCATION IN WHICHTHE CHILD NODE IS FOUND.

[INDENT][relationship type][term name][SPACE];[SPACE][PO:nnnnnnn][SPACE][relationshiptype to second parent][SPACE][second parent term name][SPACE];[SPACE][secondparent term id PO:nnnnnnn]

For example a sepal can be represented as a type of floral organ:

%floral organ ; PO:0000043
 %sepal ; PO:0000012 <flower; PO:0000007


and also as a part of the flower:

%flower ; PO:0000007
 <sepal ; PO:0000012 %floralorgan ; PO:0000043
3. Representation of synonyms.

If a term has one or more synonyms, the alternative term is representedin the flat files according to the following format:

[indentation][relationship type][termname][SPACE];[SPACE][PO:nnnnnnn][SPACE];[SPACE]synonym:[alternative name]

For example: term hair cell is a synonym of trichoblast.

 <trichoblast ; PO:0000033 ; synonym:hair cell

II. Flat file format conventions: Definition file

The following section describes the formatting used in the definition flatfiles and their meanings.

It is not mandatory to have definitions for all the terms in the ontologyflat files. However, it is suggested that every effort is made to haveone. If the definition exists, then it must contain the following:

term: the name of the PO term to which the definition refers.[term name]
goid: the term's unique identifier/accession number. [PO:nnnnnnn]
definition: the definition of the term in free text format. [definition]
definition_reference: one or more references for the definition.This includes  [Xref key]:[reference id]

A definition may also have a comment:

comment: free text  [not mandatory]

For example:

term: sepal
goid: TAIR:0000125
definition: A unit of the calyx.
definition_reference: ISBN:047124529
 
 


  

Last modified: Fri Mar 16 16:36:17 2012

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