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

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.

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).

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

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).

GtoImmuPdb Tagged Data

• Download complete immuno ligand list: Download CSV file (0.79MB) | Download TSV file (0.47MB)
• Download complete immuno target list: Download CSV file (0.31MB) | Download TSV file (0.31MB)
• Condensed GtoImmuPdb tagged targets: CSV | TSV
• Condensed GtoImmuPdb tagged ligands: CSV | TSV

Immunological Process Data

Excel spreadsheet showing mappings of GO process terms to GtoImmuPdb process categories GtoImmuPdb_GO_Process_Mappings.xls

UniProt GO Annotations in GtoImmuPdb (CSV files)

• Antigen presentation: Full Annotations
• Barrier integrity: Full Annotations
• B Cell (activation): Full Annotations
• Cellular signalling: Full Annotations
• Chemotaxis & migration: Full Annotations
• Cytokine production & signalling: Full Annotations
• Immune regulation: Full Annotations
• Immune system development: Full Annotations
• Inflammation: Full Annotations
• T cell (activation): Full Annotations
• Tissue repair: Full Annotations

Immunological Celltype Data

Cell Ontology Annotations in GtoImmuPdb (CSV files)

• B cells: Full Annotations
• Dendritic cells: Full Annotations
• Granulocytes: Full Annotations
• Innate lymphoid cells: Full Annotations
• Macrophages & monocytes: Full Annotations
• Mast cells: Full Annotations
• Natural killer cells: Full Annotations
• Other T cells: Full Annotations
• Stromal cells: Full Annotations
• T cells: Full Annotations

Downloads for 2017.5 release - NAR 2018

• List of protein targets tagged in GtoImmuPdb (NAR 2018): GtoImmuPdb_Tagged_Targets_NAR_2017.5.xls
• List of ligands tagged in GtoImmuPdb (NAR 2018): GtoImmuPdb_Tagged_Ligands_NAR_2017.5.xls
• GtoImmuPdb GO Process parent mappings (2017.5 release): GtoImmuPdb_GO_Process_Mappings_NAR_2017.5.xls
• GtoImmuPdb target (UniProt) annotations to GO (2017.5 release): GtoImmuPdb_UniProt_GO_Annotations_NAR_2017.5.xls

Other Downloads

To download data from the main GtoPdb database please visit its downloads page.

A quick search box is available at the top of all pages, which can be used to search across the whole of the Guide to PHARMACOLOGY database. When run from GtoImmuPdb, results of higher immunological relevance will be up-weighted.

The target advanced search can be accessed from the Target menu and similarly the ligand advanced search is accessed from the Ligand menu. When searching by target or ligand name, specific immunopharmacology fields can be selected from the selection menu.

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

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.

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.

Full details on Ligand Summary 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.

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
	Indicates that the ligand has been tagged in the database as being relevant to immunopharmacology

The main Immuno Processes page, details each of the main categories, with description and associate GO processes. Clicking the category titles will link to the Process Association page for that category.

The Process Association page for each category has a pull-down menu on the top-right that can be used to select the process category to view. The 'Jump to' 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

The main Immuno Cell Types page, details each of the main categories, with description and associate Cell Ontology terms. The graphical display of immuno cell types can be used to select the category to view. All categories are also listed below the schematic. Clicking the category titles will link to the Cell Type Association page for that category.

The Cell Type Association page for each category has apull-down menu on the top-right can be used to select the cell type category to view. The 'Jump to' 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.

GtoImmuPdb associates both targets and ligands to immunological diseases. The full list of diseases can be found on the Disease List page. Clicking on a disease name links to the disease summary page.

The disease displayed under the 'Immuno Disease' tab are diseases which are considered immunologically relevant, and/or are associated with targets and/or ligands of immunological significance

Associated with - Counts are displayed for the total targets the disease is associated with in GtoPdb. The counts of targets and ligands of immunological relevance aasoscited to the disease are also show.

Synonyms - Synonyms for the disease.

Description - A description/definition of the disease.

Database Links - External links to the same disease at theDisease Ontology, OMIM or Orphanet - where data is available.

Targets

Each section give details about the pathophysiology, mutation and immunopharmacology data for the target in relation to the disease. Details of the pathophysiologies in which the receptor is involved, including, where available, the ligands at the receptor which are of therapeutic use. If there are details of individual mutations that lead to the pathophysiology, these are indicted, with links back to the relevant section of the detailed target page.

Immuno ligand interaction - Where available a table of immuno-relevant ligands are shown, that also have an association to the disease. These ligands all have interaction data with the target. The approval status of the ligand is shown, along with curator comments and an indication of whether the target is consider the primary target of the ligand.

Ligands

A table of all ligands curated in GtoImmuPdb as being associated with the disease.

Approved - If the ligand is an approved drug this is indicated, along with approval bodies.

Clinical comments (Clinical Use) - The clincal use comments are general clinical comments relating to the ligand and may no necessarily be specific to the disease in question.

Clinical comments (Immuno Disease Comments) - These are curatorial comments specifically added as part of GtoImmuPdb. They gives more information on the association between the ligand and disease in the context of immunopharmacology.