About The IUPHAR/BPS Guide to IMMUNOPHARMACOLOGY

Background

These help pages describes the specific pages and content developed for the Guide to IMMUNOPHARMACOLOGY (abbreviated as GtoImmuPdb), how they are structured, and how users can access them and search for GtoImmuPdb data. For more detailed information about the Guide to IMMUNOPHARMACOLOGY please visit the GtoImmuPdb About page.

For more information on the parent Guide to PHARMACOLOGY visit the GtoPdb About, FAQ and Help pages. These include information on nomeclature terms, symbols and data downloads.

Tutorial

A tutorial for using the Guide to IMMUNOPHARMACOLOGY portal and guidance on navigating the website from the portal is available to download as a PDF.

Contact us

If you would like to get in touch with any comments, questions, error reports and suggestions please email us.

How to cite

Please refer to this page for details on how to cite the information contained in the Guide to PHARMACOLOGY and the Guide to IMMUNOPHARMACOLOGY

Guide to PHARMACOLOGY main site help

The Guide to PHARMACOLOGY Help Page provides more extensive help on using the website and understanding its contents. Please refer to this for information beyond the scope of specific Guide to IMMUNOPHARMACOLOGY features and data. Please note this will take you away from the GtoImmuPdb focussed pages.

The Data in the Guide to IMMUNOPHARMACOLOGY

Immunological Process Data

GtoImmuPdb contains data detailing immunological processes and their associations to GtoPdb targets. GtoImmuPdb has defined its own set of top-level immunological process categories against which targets in the database can be annotated and which form the basis of organising, navigating and searching for immunological processes and associations. In addition, GtoImmuPdb uses terms from the Gene Ontology (GO) to help annotated targets to these categories.

Full documentation can be found in this GtoImmuPdb immuno process data documentation (PDF).

Cell Type Data

GtoImmuPdb contains data detailing immunological cell types and their associations to GtoPdb targets. The Cell Ontology provides the formalised vocabulary against which we annotated target to cell type associations. GtoImmuPdb has defined its own set of top-level immunological cell type categories against which targets in the database can be annotated and which form the basis of organising, navigating and searching for immunological cell types and associations.

Full documentation can be found in this GtoImmuPdb immuno cell type data documentation (PDF).

Disease Data

GtoImmuPdb contains data detailing diseases and their associations to GtoPdb targets and ligands. The database currently maps these disease terms to 3 external resources: OMIM, Orphanet and the Disease Ontology. These resource help provide a formalised vocabulary against which we can annotated targets and ligands to diseases.

Full documentation can be found in this GtoImmuPdb immuno disease data documentation (PDF).

Downloading Data and Documents

Beta Release Documentation

Alpha Release Documentation

Immunological Process Data

Excel speadsheet listing annotations of GtoPdb targets versus immuno process categories: UniProt_GO_Annotation_in_GtoImmuPdb.xls

Other Downloads

GtoImmuPdb tagged targets & ligands (.xls). 26th January 2017.

Once the beta version of GtoImmuPdb is established our aim will be to provide GtoImmuPdb specific downloads on the main GtoPdb downloads page.

Seaching GtoImmuPdb

Full details on using the main site search can be found on the main GtoPdb help page.

Additional details about searching for GtoImmuPdb data will appear here in due course.

Concise Family Pages

Full details on Concise Family Pages can be found on the main GtoPdb help page.

GtoImmuPdb toggle - Within the family header, a blue 'Toggle GtoImmuPdb View' button can be used to toggle between highlighting targets that are tagged as being in GtoImmuPdb.

All target names are highlighted in blue if they are tagged in the GtoImmuPdb.

Detailed Target Pages

Full details on Detailed Target Pages can be found on the main GtoPdb help page.

Immunological Comments - General immunology related comments about the targets inclusion in the GtoImmuPdb.

Immuno Cell Type Associations - Details the main immunological cell type categories that the target is associated to. This lists specific Cell Ontology terms the target is annotated with, along with curator comments and literature references.

Immuno Process Associations - Details the main immunological process categories that the target is associated to. This lists specific Gene Ontology biological process terms the target is annotated with, along with curator comments and literature references.

Immuno Disease Associations - Details any association the target has to diseases of immunological relevance. Includes curators comments, literature references and external reference to disease resources.

Ligand Pages

Full details on Detailed Target Pages can be found on the main GtoPdb help page.

Ligand Immunopharmacology

Immunopharmacology Comments - Displays specific comments about the immnological relevancy of the ligand.

Immunopharmacology Disease - Displays any association that the ligand has to disease of immunological relevance. Included curator comments and external reference to other disease resources.

Ligand List

The Guide to PHARMACOLOGY ligand list provides a directory of ligands described in the database, divided into subsets according to chemical category. A list of approved drugs and a list of ligands labelled with a chemical group, such as a radioactive isotope, are also provided. Ligands are sorted alphabetically as far as possible.

The 'Immuno' tab provides a distinct list of all ligands that have been tagged as relevant to immunopharmacology. These ligands are also hihglighted in the 'Immuno' list and all other lists by the appearance of the immuno ligand icon next to the ligand name.

Icon/Table heading Definition
Immunopharmacology ligand Indicates that the ligand has been tagged in the database as being relevant to immunopharmacology

Targets Associated to Immuno Processes

These pages list all targets associated with our top-level immunological process categories (Immuno Processes page). The pull-down menu on the top-right can be used to select the process category to view. The 'Jump tp' links allow the user to move quickly down the page to the top of each target class section. Each row in the table shows the process association details for the named target in the first column.

GO Associations - the GO Associations column shows those GO terms that are annoted against the target. This includes the name of the term, it's GO ID (in brackets) and the 3-letter GO curation evidence code

Targets Associated to Immuno Cell Types

These pages list all targets associated with our top-level cell type categories (Immuno Cell Types page). The pull-down menu on the top-right can be used to select the cell type category to view. The 'Jump tp' links allow the user to move quickly down the page to the top of each target class section. A definition of the cell type category is displayed, clicking the 'hide definition' link on the left can remove this from view. Each row in the table shows the cell type association details for the named target in the first column.

Cell Ontology Associations - the Cell Ontology Associations column shows those Cell Ontology terms that are annoted against the target. This includes the name of the term, it's Cell Ontology ID (in brackets) - more in formation on the Cell Ontology can be found here.

Immuno Disease Associations

These pages list both targets and ligands associated to immunological diseases. The tab on the top-left switches between targets and ligands. The main table show one row per disease, with individual target or ligand associations initially hidden. The total number of associations is displayed, alongside with a condensed list of the first few targets or ligands for that disease (these link to the target or ligand pages). Clicking on the link expands the row to list all associations. The buttons on the top right can be used to show/hide all associations on the page.

Targets - Each row gives the disease name, plus external references. In the expanded view the table shows the target name, curator comments and lists ligands that the target is the primary target of and which are approved drugs.

Ligands - Each row gives the disease name, plus external references. In the expanded view the table shows the ligand name and curator comments.