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--- documentation:software:splicer [2018/03/28 13:32] – rkboyce
+++ documentation:software:splicer [2018/05/31 18:45] (current) – Converting to Wiki ericavoss
@@ Line 1: / Line 1: @@
-==== The Laertes evidence service ====
+==== The CommonEvidenceModel ====
-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 [[http://www.ohdsi.org/web/wiki/doku.php?id=projects:workgroups:kb-wg|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:
+The Common Evidence Model (CEM, formerly LAERTES) is a system that integrates numerous sources of evidence useful for investigating the association of drugs and health into a single system (see [[http://www.ohdsi.org/web/wiki/doku.php?id=projects:workgroups:kb-wg|project page]]).
-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.
+For more information on the CommonEvidenceModel refer to the [[https://github.com/OHDSI/CommonEvidenceModel/wiki|GitHub Wiki]].
-=== READ THIS FIRST!: Specific licensing information ===
-== SPLICER - Adverse Drug Reactions Extracted from United States Structured Product Labels ==
-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:[email protected]). 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.
-== EU SPC ==
-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.
-== MeSH tagged drug-HOI abstracts via PubMed/MEDLINE ==
-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.
-== Semantic MEDLINE Database ==
-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
-    * Redistribution of SKR resources in source or binary form must include this list of conditions in the documentation and other materials provided with the distribution.
-    * In any publication or distribution of all or any portion of an SKR resource (1) you must attribute the source of the tools as the resource name with the release number and date; (2) you must clearly annotate within the source code, any modification made to the resource; and (3) any subsequent distribution of program, tool, or material based on the resource, must be accomplished within the context of an open source set of terms and conditions such as the GNU General License.
-    * Bugs, questions, and issues relating to an SKR resource should be directed to the most recent of the chain of entities that may have modified and re-distributed this resource.
-    * You shall not assert any proprietary rights to any portion of an SKR resource, nor represent it or any part thereof to anyone as other than a United States Government product.
-    * The name of the U.S. Department of Health and Human Services, National Institutes of Health, National Library of Medicine, and Lister Hill National Center for Biomedical Communications may not be used to endorse or promote products derived from any SKR resource without specific prior written permission.
-    * Neither the United States Government, U.S. Department of Health and Human Services, National Institutes of Health, National Library of Medicine, Lister Hill National Center for Biomedical Communications, nor any of its agencies, contractors, subcontractors or employees of the United States Government make any warranties, expressed or implied, with respect to any SKR resource, and, furthermore, assume no liability for any party's use, or the results of such use, of any part of these tools.
-These terms and conditions are in effect as long as the user retains any part of any SKR resource.
-== FAERS spontaneous report counts and pharmacovigilance signals ==
-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).
-== Comparative Toxicogenomics Database Drug-disease associations ==
-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.
-== Information on all Laertes evidence services [GET]==
-<code>
-http://YOUR SERVER/WebAPI/evidence/<source>/info
-</code>
-Example: http://api.ohdsi.org/WebAPI/evidence/CS1/info
-== Evidence  by drug concept id (any level in the drug hierarcchy) [GET]==
-<code>
-http://YOUR SERVER/WebAPI/evidence/<source>/drug/{CONCEPT ID}
-</code>
-Example: http://api.ohdsi.org/WebAPI/evidence/CS1/drug/752061
-== Evidence by HOI concept id [GET]==
-<code>
-http://YOUR SERVER/WebAPI/evidence/<source>/hoi/{CONCEPT ID}
-</code>
-Example: http://api.ohdsi.org/WebAPI/evidence/CS1/hoi/320073
-== Evidence by concatenated drug and HOI concept id [GET]==
-<code>
-http://YOUR SERVER/WebAPI/evidence/<source>/hoi/{DRUG CONCEPT ID}-{HOI CONCEPT ID}
-</code>
-Example: http://api.ohdsi.org/WebAPI/evidence/CS1/drughoi/19059744-381591
-== Evidence with any OHDSI concept id representing an RxNorm or SNOMED concept==
-<code>
-http://api.ohdsi.org/WebAPI/evidence/<source>/{DRUG or HOI CONCEPT ID}
-</code>
-Example: http://api.ohdsi.org/WebAPI/evidence/CS1/752061