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Pharmacovigilance: Drugs, Toxics and Adverse Effects Databases

The most important databases about drugs and chemical compounds. Introduction to drug design subject. Bachelor's Degree in Biomedical Engineering (UPF) 2016-17
by

Miguel Angel Mayer

on 21 November 2016

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Transcript of Pharmacovigilance: Drugs, Toxics and Adverse Effects Databases

Medical Subject Headings (MeSH)
International Classifications of diseases
What is a standard?
What is a terminology?
Coding systems and terminologies are structured set of terms
designed to describe more precisely and in an unambiguous way
different kinds of information...
from diagnosis and
treatment
of patients in clinical care,
to structure and semantics of clinical documents
or terminologies and
thesaurus used to
retrieve documents
from biomedical databases.
ICD: “International Statistical Classification of Diseases and Related Health Problems” (Published by the WHO)
Current versions: ICD-9 (ICD-9 CM) and ICD-10

In its diverse forms, has a legal status in many jurisdictions

Used worldwide for:
Morbidity and mortality statistics
Reimbursement systems
Decision support in health care
At the beginning it included only diagnostics currently signs, symptoms, physical examination findings, social problems and external causes of diseases
It is divided in chapters, including related conditions
Each chapter includes categories that are divided in concrete diagnostics
The idea is to cover all the possible diagnostics currently known
http://apps.who.int/classifications/icd10/browse/2010/en
SNOMED-CT: Systematized Nomenclature for Medicine-Clinical Terminology

Allows in a consistent way storing, indexing, retrieving and aggregation of clinical data among different specialties and places of clinical healthcare (ICD, ACIP, LOINC, NANDA, etc).

It is considered by some to be the most comprehensive, multilingual clinical healthcare terminology in the world.

Integrated in the UMLS
Why the need for coded terminologies and standards?
The language of
biomedicine and health is as complex and extensive
as the concepts it represents and it is constantly changing to include new knowledge, skills, and capabilities.

Data analysis:
a code identifies a biomedical concept in a unique way making possible the statistical analysis

To avoid
data redundancy
in storing systems

To make interoperability possible:
many systems may use the same (or “translated”) codification to communicate each other without ambiguity
UMLS
(Unified Medical Language System)
Promoted by the National Library of Medicine (NLM)
(as PubMed and Medline)

It is a
Metathesaurus
(combination of diverse thesaurus) linking diverse biomedical terminologies and databases

Integrates the main international terminologies in Biomedicine in a common structure

and the "mapping" among different terminologies

One important aim is to contribute in the development of electronic systems that integrate and understand each other such as EHR, Biomedical DB or decision support systems.

Include: MeSH, ICD-9, ICD-10, SNOMED, LOINC....
http://www.nlm.nih.gov/research/umls/
Standard set of bibliographic headings for biomedical applications, of reference in Biomedicine
MeSH thesaurus is a controlled vocabulary produced by the NLM used for indexing, cataloging, and searching for biomedical and health-related information and documents
It is organized in a tree hierarchy with semantic families and relations
Each MeSH record consists of one or more concepts, and each Concept consists of one or more synonymous terms
The relation between the descriptors are:
Hierarchical:
parents and children
Relational:
different parents and children but interrelated
Synonyms:
different words with the same meaning

It is possible to combine descriptors MeSH with
“subheadings”
Integration languages in
Biomedical Information
SNOMED-CT
http://snomed.dataline.co.uk/
*Source: 3M Health Information Systems. Role of Standards Terminologies
Controlled vocabulary thesaurus for indexing concepts
Pharmacovigilance: Drugs &
Adverse Effects Databases
& Terminologies


Miguel A. Mayer
Research Programme on Biomedical Informatics
IMIM-Universitat Pompeu Fabra
mmayerp

Objectives:

- To mention the main Databases
and terminologies related to drugs
and adverse effects (including MeSH or ICD10)

- To gather different useful resources related to drugs and toxics
DrugBank
http://www.drugbank.ca
The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
T3DB
http://www.t3db.ca
FooDB
http://foodb.ca
HMP
The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body.
The database currently houses 3,673 toxins described by 41,729 synonyms, including pollutants, pesticides, drugs, and food toxins, which are linked to 2,086 corresponding toxin target records.
http://hmdb.ca
Anatomical Therapeutic Chemical Classification System (ATC)
http://www.whocc.no/atc_ddd_index/
World Health Organization (WHO)
TOXNET
http://www.accessdata.fda.gov/scripts/cder/drugsatfda/
Drugs@FDA
Drugs@FDA allows you to search for official information about FDA approved innovator and generic drugs and therapeutic biological products.
IntSide
SIDER 4.1:
Side Effect Resource
PharmGKB
https://www.pharmgkbInsi.org/
The PharmGKB is a pharmacogenomics knowledge resource that encompasses clinical information including dosing guidelines and drug labels, potentially clinically actionable gene-drug associations and genotype-phenotype relationships. PharmGKB collects, curates and disseminates knowledge about the impact of human genetic variation on drug responses
IntSide is a web server to elucidate the molecular processes involved in drug side effects through the integration of chemistry and biology.
http://intside.irbbarcelona.org/
http://sideeffects.embl.de/

Side effects are phenotypic responses of the human organism to drug treatment

Pharmacological and medical research would greatly benefit from the integration of side effect data with other public sources in medicine and chemical biology
PubChem
https://pubchem.ncbi.nlm.nih.gov/search/
http://www.ncbi.nlm.nih.gov/pubmed
http://www.meddra.org/
Standardised medical terminology to facilitate sharing of regulatory information internationally for medical products used by humans.
http://www.ema.europa.eu/ema/index.jsp?curl=pages/includes/medicines/medicines_landing_page.jsp
http://zinc.docking.org/search/
ZINC
The ZINC database, a curated collection of commercially available chemical compounds prepared especially for virtual screening
EMA
The ATC/DDD system is a tool for exchanging and comparing data on drug use at international, national or local levels.
ATC
The
DDD
is the assumed average maintenance dose per day for a drug used for its main indication in adults.
A DDD will only be assigned for drugs that already have an ATC code.
http://www.ncbi.nlm.nih.gov/mesh
The
PubChem substance
database contains chemical structures, synonyms, registration IDs, description, related urls, database cross-reference links to PubMed, protein 3D structures, and biological screening results. If the contents of a chemical sample are known, the description includes links to
PubChem Compound.
The PubChem Compound Database contains validated chemical depiction information that is provided to describe substances in PubChem Substance.
resource for searching databases on toxicology, hazardous chemicals, environmental health, and toxic releases
http://toxnet.nlm.nih.gov/
Terapeutics Targets Database
http://bidd.nus.edu.sg/group/ttd/ttd.asp
detailed toxin data with comprehensive toxin target information
Some standards in biomedicine
Protect ADR
Database
PROTECT consists of 34 public and private partners coordinated by the European Medicines Agency. The database lists all of the adverse drug reactions (ADRs) that are included in the summary of product characteristics (SmPC) for drugs that have authorization to be marketed in the EU
http://www.imi-protect.eu/methodsRep.shtml
ICD10 website of the World Health Organization
AEMPS
http://www.aemps.gob.es/cima/pestanias.do?metodo=accesoAplicacion
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