An immunologically friendly classification of non-peptidic ligands

Abstract

The Immune Epitope Database (IEDB) freely provides experimental data regarding immune epitopes to the scientific public. The main users of the IEDB are immunologists who can easily use our web interface to search for peptidic epitopes via their simple single-letter codes. For example, 'A' stands for 'alanine'. Similarly, users can easily navigate the IEDB's simplified NCBI taxonomy hierarchy to locate proteins from specific organisms. However, some epitopes are non-peptidic, such as carbohydrates, lipids, chemicals and drugs, and it is more challenging to consistently name them and search upon, making access to their data more problematic for immunologists. Therefore, we set out to improve access to non-peptidic epitope data in the IEDB through the simplification of the non-peptidic hierarchy used in our search interfaces. Here, we present these efforts and their outcomes. Database URL: http://www.iedb.org/.

Figure 1.

Overall structure of the revised chemical tree whereby the highest level is subdivided into organic and inorganic chemicals. The inorganic and organic branches are further subdivided into the most prominent and intuitive categories. The number of entries per level is indicated at the end of each branch’s label.

Figure 2.

(a) A high-level breakdown of the inorganic molecular entity branch of the structure tree. Some of these are terminal branches, while others are subdivided into more specific structures for greater specificity. The number of entries per level is indicated at the end of each branch’s label.

Figure 2.

(b) A high-level breakdown of the carbohydrate and carbohydrate derivative, and lipid branches of structure tree. Both of these are children of ‘organic molecular entity’. Some of these are terminal branches, while others are subdivided into more specific structures for greater specificity. The number of entries per level is indicated at the end of each branch’s label.

Figure 2.

(c) A high-level breakdown of the nucleic acid and related molecular entity, nitrogen molecular entity, sulfur molecular entity, nitrogen molecular entity, sulfur molecular entity branches of the structure tree. All of these are the children of ‘organic molecular entity’ Some of these are terminal branches, while others are subdivided into more specific structures for greater specificity. The number of entries per level is indicated at the end of each branch’s label.

Figure 2.

(d) A high-level breakdown of the acid an hydride, alcohol, aromatic molecular entity, carbonyl molecular entity, non-aromatic ether and other molecular entity branches of the structure tree. All of these are children of ‘organic molecular entity’. Some of these are terminal branches, while others are subdivided into more specific structures for greater specific structures for greater specificity. The number of entries per level is indicated at the end of each branch branch’s label.

Figure 3.

(a) The ‘application’ role class of the revised role tree, excluding the drug branch, which is further subcategorized into the most prominent application. Some of these are terminal branches, while others are subdivided into more specific application types for greater specificity. The number of entries per level is indicated at the end of each branch’s label.

Figure 3.

(b) The ‘drug’ branch of the ‘application’ role class of the revised role tree, which is further subcategorized into the most prominent applications. Some of these are terminal branches, while others are subdivided into more specific application types for greater specificity. The number of the entries per level is indicated at the end of each branch’s label.

Figure 3.

(c) The ‘biological role classes of the revised role tree, which is further subcategorized into the most prominent biological functions. Some of these are terminal branches, while others are subdivided into more specific biological role types for greater specificity. The number of entries per level is indicated at the end of each branch’s label.

Figure 3.

(d) The ‘chemical role’ role class of the revised role tree, which is further subcategorized into the most prominent chemical roles. Some of these are terminal branches, while others are subdivided into more specific chemical roles. Some of these are terminal branches, while others are subdivided into more specific chemical role types for greater specificity. The number of number of entries per level is indicated at the end of each branch’s label.

Figure 4.

User testing comparison of old and new non-peptidic trees, where users were tasked in locating 20 non-peptidic entities across the two trees while being timed. Statistical significance was achieved with P < 0.005, as all participants consistently located more entities in the new tree.