Overview of query methodology
Pharmacorank is an open search tool for the retrieval of medication-protein target pairs that are either known or predicted to be relevant in the treatment of a queried disease. The functions of the proteins associated with the selected disease are to prioritize the search results. Priority scores are converted to pertinency scores which are the estimated probabilities that the protein targets and their associated medications are relevant in the treatment of the selected disease. Medications which are currently not known to treat the selected disease are labeled as such and are considered as possible repositioning candidates.
Interactive text queries are enabled from the home page. The query input box has an autocomplete feature where the corresponding Disease Ontology term is identified as one types a disease. The results of pre-run searches are available in the Downloads area.
For examples of queries, please refer to the example queries page.
The following is a partial list of data sources on which the tool relies.
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.
Disease Ontology provides an open source ontology for the integration of biomedical data that is associated with human disease.
DrugCentral is an online drug information resource created and maintained by Division of Translational Informatics at University of New Mexico in collaboration with the IDG.
DisGeNET is a database that integrates information of human gene-disease assocociations (GDAs) and variant-disease associations (VDA) from various repositories including Medelian, complex and environmental diseases.
Gene Ontology (GO) is resource that provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from humans to bacteria.
InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites.
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
MEDI (MEDication Indication) is an ensemble medication indication resource for primary and secondary uses of electronic medical record (EMR) data.
OMIM, or Online Mendelian Inheritance in Man®, is a comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily.
RxNorm provides normalized names for clinical drugs and links its names to many of the drug vocabularies commonly used in pharmacy management and drug interaction software, including those of First Databank, Micromedex, Multum, and Gold Standard Drug Database.
UniProt Keywords constitute a controlled vocabulary with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.
UniProt sequence annotations describe regions or sites of interest in the protein sequence, such as post-translational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references.
