Data warehouse for drug discovery
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README.md

#TargetMine TargetMine is an integrated data warehouse system for target discovery based on the InterMine framework. See below for more details.

Web site: http://targetmine.mizuguchilab.org/

Reference: Chen Y-A, Tripathi LP, Mizuguchi K (2016) An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. Database (Oxford). 2016 Mar 17;2016. pii: baw009.
doi: 10.1093/database/baw009

Chen Y-A, Tripathi LP, Mizuguchi K (2011) TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery. PLoS ONE 6(3): e17844.
doi:10.1371/journal.pone.0017844

#Installation See the INSTALL file for installation instructions.

#TargetMine Source Distribution Copyright (C) 2011-2016 by The Mizuguchi Laboratory.

TargetMine requires the InterMine library. A modified version of InterMine is included in this distribution. (See 'Customized InterMine Library' below for details. The three directories, bio, imbuild and intermine, contain the InterMine library.)

#InterMine

A powerful open source data warehouse system.

InterMine Documentation

In order to improve the chance of continued funding for the InterMine project it would be appreciated if groups that use InterMine or parts of InterMine would let us know (email [info[at]flymine.org](mailto:info flymine.org)).

Copyright (C) 2002-2017 FlyMine

This product includes software developed by the Apache Software Foundation.

#Licenses TargetMine is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License.

See LICENSE for licensing information.

InterMine is an open source project distributed under the GNU Lesser General Public Licence.

See LICENSE.intermine and LICENSE.intermine.LIBS for licensing information.

#Customized InterMine Library The following files were modified.

  • bio/webapp/resources/webapp/WEB-INF/classDescriptions.properties
  • bio/postprocess/main/src/org/intermine/bio/postprocess/PostProcessOperationsTask.java
  • bio/webapp/src/org/intermine/bio/web/logic/OrthologueConverter.java
  • intermine/web/main/src/org/intermine/web/struts/BuildBagAction.java
  • intermine/web/main/src/org/intermine/web/struts/BuildBagForm.java

The following files were added.

  • bio/postprocess/main/src/org/intermine/bio/postprocess/AssociateGeneAndIPC.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/CalculateBioThemeBackground.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/CoExpressionInteraction.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/HierarchicalClustering.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/IntegratedPathwayClustering.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/NetworkAnalysisTool.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/PpiDruggability.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/RemoveCompoundCasRegistryNumber.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/TranscribeDrugBankTargets.java
  • bio/postprocess/main/src/org/intermine/bio/postprocess/TranscribeNcbiGeneId.java
  • bio/webapp/src/org/intermine/bio/web/logic/ProteinOrthologConverter.java