Semantic resources project/Antibodies/Antibody OBI Terms

Initial Model
Our initial modeling and exploration is detailed on a separate page; this work has been superseded by the revised model, presented below.

Refined Model
Begin with a high-level outline of the ontology and the graphical notation.



This is described, in OWL, with the file:

There are four parts to our representation:
 * 1) Specificity
 * 2) Offer to Sell
 * 3) Creation
 * 4) Monoclonal Creation
 * 5) Polyclonal Creation

Specificity
Typically, two separate fields are provided for specificity: one is a description of the antigen, or the epitope on the antigen, to which the antibody shows specificity. The second is a more general term, such as from PRO, denoting the class of proteins which the the antibody is believed to recognize.

These are translated into two separate assertions, one about the protein (and its propensity to be 'recognized' by the antibody), and the other about the antibody itself (and its disposition to recognize members of the antigen class).



A demonstration of this representation is given in

Definitions
/Old Definitions

Definitions from the owl file above are being converted into tabular format here, for eventual submission as terms to OBI.

Light blue lines denote occurrents (in this case, mostly planned processes).

Orange lines denote information content entities or other GDCs.

Pink lines denote continuants, such as roles, dispositions, or material entities.

Annotation Workflow
Our workflow has several steps.


 * 1) We start with a database dump of the antibody information and offer sheets.
 * 2) We then export this database file(s) to a simple RDF transliteration.
 * 3) Automatic dictionaries and pattern matching schemes are run on the RDF properties of each antibody, to discover:
 * 4) Catalog Numbers
 * 5) Supplier Names
 * 6) Protein names (for specificity)
 * 7) Species names
 * 8) experimental method (usage) identifiers
 * 9) Supplier instructions (format, temperature, etc.)
 * 10) Creation Information (clonality, clone number, isotype)
 * 11) Epitope descriptions
 * 12) Since these patterns are noisy and difficult to match exactly, each set of annotations for an antibody record is then reviewed by one or more human annotators using an Annotation Software Package written for this project.
 * 13) The reviewed and accepted annotations are exported into a tabular format with fields corresponding to the parts of the OBI model described above.
 * 14) Finally, scripts are used to convert the tabular format into OBI-compliant OWL documents.