Guidelines and Information About Therapy Experiments (GIATE) is a data standard for recording data about therapy experiments. It is being promoted by the Antibody Society, as a data standard for antibody therapy experiments but it has become apparent that the scope of materials used in antibodies as therapeutic agents, means that the data standard can equally be used to describe a wide range of therapeutics.
GIATE categorises the information about therapy experiments into three classes, that is, information about the target, therapy agent and models used to test the therapy. Nested within these classes are additional classes describing different aspects and properties of the parent class. Therefore, a logical representation of GIATE would be a tree, with three main branches, which stems into smaller branches and leaves.
The first branch addresses the information about the targets of the therapeutic. The target may be a gene product, an organic chemical or a small molecule. There may be more then a single target in a course of therapy, and these targets may be a combination of any of these classes. Different pieces of information are relevant to the different target types. For example, if the target is a protein, one property of the protein can be the UNIPROT accession number. If the target is a small molecule, a property used to describe it could be the SMILE format. The targets would have a few properties in common, for example, the binding site to which the therapeutic agent would bind.
The second branch addresses the information about the therapeutic agents. Again, there may be different types of agents, with the appropriate properties. For example, an antibody would be a type of therapeutic agents, and there would be component types to describe the components of the antibody itself.
The third branch addresses the models used to test the therapy. This consists of molecular, cellular models, animal and clinical models. There are different properties which addresses each model, from the experimental conditions of the molecular models, to the species and target homology to man of the animal, to the MABEL and NOAEL information for the patient. For each of the models, GIATE specifies a set of measurements for describing the quantities of the targets and therapeutic agents, the methods of administration, and the effects and outcomes of administering the agents.
The goal of GIATE is to form consistent summaries of therapeutics, by recording the important elements required to achieve a specific set of results. A set of summaries recorded according to GIATE would be comparable in every aspect, from target to models. The universal adoption of a data standard such as GIATE allows the researchers from different organizations and fields to overcome the difficulties in data sharing, which occurs when researchers collect different sets of information according to their habits, or organizations' cultures.
As mentioned above, GIATE is a set of properties that have been organized to describe different aspects of a therapy, from the target, the agent and the models for testing. This provides researchers with a consistent set of information to record. The organization of the tree allows users of different expertise to address only the branches they are interested in. It also allows organizations to build more branches on the GIATE root, to address additional pieces of information they are interested in.
In addition, each property in GIATE is listed with it's own description. This description carries a definition of the object of the property (what is being described), the property itself (what type of information about the object), as well as the appropriate data range for recording the information. For example, the property "Protein UNIPROT ID" carries a definition of the object (eg "Proteins are a group of complex organic.. etc"), a definition of the property UNIPROT id (eg "The UniProt Knowledgebase (UniProtKB) provides a central database.. etc"). The description of the property also states that the valid range of data used to fill the property would be "One or more characters and/or numbers that are used to identify...etc".
Binding each property to it's description addresses the issue of understanding exactly what is required. Researchers across different fields may use the same term for describing different elements of their research; the property's description provides a singular definition of the property for which information should be recorded.
Researchers can
1) use GIATE purely as a reference tool, to inspect the elements of an experiment design that should be taken account of.
2) agree to collect data according to GIATE, or parts of GIATE. This will enable them to view summaries of each other's work, as far as GIATE allows.
The GIATE is kindly hosted by Genscript at this address. We are extending the GIATE by building the GIATE notebook, which is a lab book style software.
The GIATE notebook is a Java programme allowing users to view and save their data according to the elements of GIATE on a standalone machine. There are sections for adding comments, and links to files and URLs. A user can save their experimental data and present it along with any supplementary materials. It can be downloaded from the Antibody Society website.
The GIATE tree viewer of web version is implemented by JQuery and Xquery techniques. The first loading of the web page may be slightly slow because it will take time to read the data of GIATE notebook and built up the tree, while the data are approximate 1 MB in size. The tree viewer has been tested on several different modern web browsers, and it should be compatible with Internet Explorer (6, 7, 8), Firefox (>3.0), Opera (>9.0), Apple Safari, and Google Chrome.