Animal Trait Ontology Project
Developing Frameworks and Tools for the Livestock Community

A Gentle Guide to ATO Developers

Data Representation

1. Concept

The ATO is composed of a simple data structure called the Directed Acylic Graph (DAG). This structure is a type of hierarchy where the biological concepts are organized as a network tree structure in which the nodes at the top (root) of the tree are more general cases of specific terms at the bottom (leaves) of the structure.

Like a simple hierarchy, children are not allowed to be their own ancestors; hence cycles are forbidden. However, unlike a simple hierarchy, child nodes are allowed to have more than one parent node, thus allowing multiple child to parent relationships.

2. Use of term-term relationships in the ontology tree

Is_a (or Instance_of): This relationship is used to indicate the relationship between a specific term to a more general one. For example average daily feed intake is an instance_of feed intake, which is an instance_of production.

3. Syntax:

Parent-child relationships between terms are represented by indentation: 
parent_term
child_term
Instance_of relationship represented as follows: 
%term0
%term1 %term2
This is read as term1 being an instance of term0 and also an instance of term2.

Combined Instance relationship and Part-of relationship represented as follows: 

%term0
%term1 <  term2 < term3
This is read as term1 being an instance of term0 and also a part-of term2 and term3.

Data Management

The ATO data is stored and managed with the relational databases, MySQL and Postgres. The data input and modification is performed using the Collaborative Ontology Building (COB) editor coupled with Postgres. In order to perform edits, one must register as an ATO curator to obtain the appropriate access privileges. The ATO data can be freely browed with the Amigo web visualization tool coupled with the MySQL database.

Contributing to the ATO

The Collaborative Ontology Building (COB) editor provides mechanisms for multiple participants to work together, therefore it is designated as the official ATO editor for the consortium.

1) Use of the COB editor:

Ontology editors allow curators to browse, search, visualize, and edit ontologies. The Collaborative Ontology Building (COB) tool, developed jointly by the USDA Bioinformatics Coordination team and the Artificial Intelligence Laboratory of Iowa State University, is an ontology editor with additional capabilities such as editing of the names, definitions, synonyms, relationships, etc. The COB editor can support collaborative ontology building efforts among researchers in disparate locations by allowing curators to check out packages (or certain parts of the ontology). It also has a concurrent access and locking mechanism that prevents curators from editing a particular term at the same time. This COB editor can be downloaded to a local machine which then gives a user access to a centrally located database. Depending on access rights, the user may be in edit or view-only mode.

2) Adding trait terms:

The inclusion of new traits into the ontology is important to the growth of the ATO. New trait information comes from journal articles, books, local researcher archives, and other miscellaneous sources. The inclusion of new traits should be an objective measure of the term information as it appears in the original reference. If there are multiple trait terms for a particular trait, the most commonly used (as indicated by different sources or experts) trait should be used as the trait name. Less commonly used terms, should be indicated in the synonym or custom name fields. The insertion of a new trait should be made into a proper ontology category.

3) Change trait properties:

The current trait properties include trait name, trait description, synonym, measurement, scale unit, custom name, and abbreviation. The need to update the properties associated with traits will be evident once new sources of trait information become available. The inclusion of the updated information should be an objective measure of the property information as it appears in the original reference. If there are multiple values for a particular property, the most commonly used (as indicated by different sources or experts) property should be used. Multiple properties may be indicated with the use of a ‘;’ to separated the records.

4) Annotate trait and trait categories:

The trait categories can be changed, cloned, moved, deleted, etc. using the COB editor. The editor allows users to make changes to the properties associated with a trait. The changes can be committed replacing any previous edits. Cloning allows traits and it’s associated properties to be used again in another area of the ontology. For instance, if a trait is used in one ontology but has the same properties as a trait in another classification, then that term can be cloned. Moving traits and categories around to other locations in the ontology is also allowed. The deletion of properties is also possible as the ontology is expected to continuously evolve.

5) Improve the structure:

The structure of the ATO currently includes six top level terms: production, reproduction, exterior, development, product quality, and immune function. These categories and subcategories currently serve the needs of researchers in the general animal science field. Future improvements to this structure will likely be needed with the evolution of research in animal science and other related fields, such as biomedical sciences, animal model studies, germ plasm preservations, zoology, etc. The facilitation of these changes may be implemented through effective communications between researchers and curators of the ATO.

6) Solve discrepancies or disagreements:

Discrepancies and disagreements among users of the ATO is expected as the ATO grows. To facilitate the mediation process, emails, meetings, discussion forums, etc. may be used to communicate the disagreements between experts for a given trait. Once a consensus has been made, the update will be implemented in the ATO. The history of the discussions may be kept as part of the documentation of ATO for future reference.

How to participate

If you are interested in contributing to the ATO, first of all you should contact James Reecy (jreecy@iastate.edu) to obtain consent. Then you should download the COB editor from http://www.animalgenome.org/bioinfo/tools/share/COB/, obtain a login and password, and join the consortium discussion forum or listserv.