Documentation
Common Data Model (CDM)
Convert Database to CDM (ETL)
Tool Specific Documentation
Common Data Model (CDM)
Convert Database to CDM (ETL)
Tool Specific Documentation
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Laertes (Largescale Adverse Effects Related to Treatment Evidence Standardization) is a system that integrates numerous sources of evidence useful for investigating the association of drugs and health into a single system (see project page). The REST service calls provide for summary and drill down queries of evidence sources. Use of these services requires compliance with the specific licensing requirements of the evidence sources (see below). Please be sure to cite the following paper for any work you publish or present that used Laertes:
Boyce. RD., Ryan. PB., Noren. N., et al., Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest. Drug Safety. 2014. Volume 37, Issue 8 (2014), Page 557-567. DOI: 10.1007/s40264-014-0189-0, PubMed PMID: 24985530. PMCID: PMC4134480.http://link.springer.com/article/10.1007%2Fs40264-014-0189-0.
SPLICER data are licensed under http://creativecommons.org/licenses/by-nc-sa/4.0/ meaning they are for non-commercial work only. If you are a commercial organization, please contact Regenstrief Institute for licensing information (mailto:allenkat@regenstrief.org). Non-commercial users please be sure to cite the following paper for any work you publish or present that used SPLICER data:
Duke J, Friedlin J, Li X. Consistency in the safety labeling of bioequivalent medications. Pharmacoepidemiol Drug Saf. 2013 Mar;22(3):294-301. doi:10.1002/pds.3351. Epub 2012 Oct 8. PubMed PMID: 23042584.
The EU SPC source provides adverse drug events extracted from EU SPCs by the [PROTECT](http://www.imi-protect.eu/about.shtml) collaborative. See the online documentation for the [PROTECT Adverse Drug Reactions Database](http://www.imi-protect.eu/adverseDrugReactions.shtml) for a liability disclaimer.
The scripts in this folder retrieve PubMed/MEDLINE records for indexed literature reporting adverse drug events. The data is derived by the Laertes developer using a licensed copy of the publicly available PubMed database.
Please note the following licensing information:
NLM represents that its data were formulated with a reasonable standard of care. Except for this representation, NLM makes no representation or warranties, expressed or implied. This includes, but is not limited to, any implied warranty of merchantability or fitness for a particular purpose, with respect to the NLM data, and NLM specifically disclaims any such warranties and representations.
NLM data are produced by a U.S. Government agency and include works of the United States Government that are not protected by U.S. copyright law but may be protected by non-US copyright law, as well as abstracts originating from publications that may be protected by U.S. copyright law.
NLM assumes no responsibility or liability associated with use of copyrighted material, including transmitting, reproducing, redistributing, or making commercial use of the data. NLM does not provide legal advice regarding copyright, fair use, or other aspects of intellectual property rights. Persons contemplating any type of transmission or reproduction of copyrighted material such as abstracts are advised to consult legal counsel.
Also, please site the following paper for any work you publish or present that used this data source:
Avillach P, Dufour JC, Diallo G, Salvo F, Joubert M, Thiessard F, Mougin F, Trifirò G, Fourrier-Réglat A, Pariente A, Fieschi M. Design and val idation of an automated method to detect known adverse drug reactions in MEDLINE: a contribution from the EU-ADR project. J Am Med Inform Assoc. 2013 May 1;20(3):446-52. doi: 10.1136/amiajnl-2012-001083. Epub 2012 Nov 29. PubMed PMID: 23195749; PubMed Central PMCID: PMC3628051.
The [Semantic MEDLINE Database](http://skr3.nlm.nih.gov/SemMedDB/) is a repository of semantic predications (subject-predicate-object triples) extracted by SemRep, a semantic interpreter of biomedical text. The webservice provides data queried from the Semantic MEDLINE Database and PubMed/Medline. Please cite the following paper in any publications or presentations of work that uses the data:
Kilicoglu H, Rosemblat G, Fiszman M, Rindflesch TC. Constructing a semantic predication gold standard from the biomedical literature. BMC Bioinformatics. 2011 Dec 20;12:486. doi: 10.1186/1471-2105-12-486. PubMed PMID: 22185221; PubMed Central PMCID: PMC3281188.
In addition to the licensing requirements of the “MeSH tagged drug-HOI abstracts via PubMed/MEDLINE” service (see above), the following use restrictions apply to users of the data provided by this resource:
Use of Semantic Knowledge Representation (SKR) Resources
These terms and conditions are in effect as long as the user retains any part of any SKR resource.
Please be sure to cite the following paper for any work you publish or present that used AERS count or signal data:
N. P. Tatonetti, P. P. Ye, R. Daneshjou, R. B. Altman, Data-Driven Prediction of Drug Effects and Interactions. Sci Transl Med 4, 125ra31–125ra31 (2012).
Legal Notices
The Comparative Toxicogenomics DatabaseTM (CTDTM) is provided to enhance knowledge and encourage progress in the scientific community. It is to be used only for research and educational purposes. Medical treatment decisions should not be made based on the information in CTD.
Any reproduction or use for commercial purpose is prohibited without the prior express written permission of the MDI Biological Laboratory and NC State University.
This data and software are provided “as is”, “where is” and without any express or implied warranties, including, but not limited to, any implied warranties of merchantability and/or fitness for a particular purpose, or any warranties that use will not infringe any third party patents, copyrights, trademarks or other rights. In no event shall the MDI Biological Laboratory nor NC State University, nor their agents, employers or representatives be liable for any direct, indirect, incidental, special, exemplary, or consequential damages however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way or form out of the use of this data or software, even if advised of the possibility of such damage.
THE COMPARATIVE TOXICOGENOMICS DATABASE and CTD are trademarks of the MDI Biological Laboratory and NC State University. All rights reserved.
Copyright 2002-2012 MDI Biological Laboratory. All rights reserved.
Copyright 2012-2016 MDI Biological Laboratory & NC State University. All rights reserved.
See http://ctdbase.org/about/legal.jsp for further information and notices.
http://YOUR SERVER/WebAPI/<source>/evidence/info
http://YOUR SERVER/WebAPI/<source>/evidence/drug/{CONCEPT ID}
Example: http://api.ohdsi.org/WebAPI/evidence/CS1/drug/752061
http://YOUR SERVER/WebAPI/<source>/evidence/drugrollup/ingredient/{CONCEPT ID}
Example: http://api.ohdsi.org/WebAPI/evidence/CS1/drugrollup/ingredient/1000632“
http://YOUR SERVER/WebAPI/<source>/evidence/drugrollup/clinicaldrug/{CONCEPT ID}
Example: http://api.ohdsi.org/WebAPI/evidence/CS1/drugrollup/clinicaldrug/19074181”
http://YOUR SERVER/WebAPI/<source>/evidence/drugrollup/brandeddrug/{CONCEPT ID}
Example: http://api.ohdsi.org/WebAPI/evidence/CS1/drugrollup/brandeddrug/1000640“
http://YOUR SERVER/WebAPI/<source>/evidence/hoi/{CONCEPT ID}
Example: http://api.ohdsi.org/WebAPI/evidence/CS1/hoi/320073
http://YOUR SERVER/WebAPI/<source>/evidence/hoi/{DRUG CONCEPT ID}-{HOI CONCEPT ID}
Example: http://api.ohdsi.org/WebAPI/evidence/CS1/drughoi/19059744-381591
http://api.ohdsi.org/WebAPI/evidence/CS1/{DRUG or HOI CONCEPT ID}