Database Updates

Mammalian Quartely Updates
Mammalian Public datasets
Plant Optional Updates
Yeast Optional Updates
Mapfile Updates

How to Import Update Files

Unzip if the file has extension .zip
Open Pathway Studio and go to the menu Database to call Import Wizard
Choose "Other" on the first page of the Import Wizard and click "Next"
For files marked in the File type column as "RNEF XML" choose "Resnet" option on the second page of the wizard. RNEF XML files can have extension .xml, .gpp. or .rnef
For files marked "text" in the File type column choose "Plain text" option on the second page of the Wizard. Plaintext files have extension .txt
Click Next button on all other Import Wizard pages to finish the import

Mammalian Quarterly Updates

Title	Date	Type	Size	File type
ResNet 5 update 2008 Q3 *	Nov 6, 2008	Database Update	10 Mb	ZIP/GPP
Quarterly update for the Mammalian ResNet - quarter 3 of 2008
ResNet 5 update 2008 Q2 *	Jul 30, 2008	Database Update	12 Mb	ZIP/GPP
Quarterly update for the Mammalian ResNet - quarter 2 of 2008
ResNet 5 update 2008 Q1 *	Apr 8, 2008	Database Update	16 Mb	ZIP/GPP
Quarterly update for the Mammalian ResNet - quarter 1 of 2008
ResNet 5 update 2007 Q4 *	Jan 8, 2008	Database Update	8 Mb	ZIP/GPP
Quarterly update for the Mammalian ResNet - quarter 4 of 2007
ResNet 5 update, 2007 Q3 *	Oct 3, 2007	Database Update	13 Mb	ZIP/GPP
Mammalian database update, quarter 3 of 2007
ResNet 5 update 2007 Q2 *	Jun 8, 2007	Database Update	11 Mb	ZIP/GPP
Quarterly update for the Mammalian ResNet - quarter 2 of 2007
ResNet 5 update 2007 Q1 *	Apr 15, 2007	Database Update	23 Mb	ZIP/GPP
Quarterly update for the Mammalian ResNet - quarter 1 of 2007

Public datasets in RNEF XML format for mammal database

Title	Date	Type	Size	File type
Protein annotation and interactions from Entrez Gene *	Jan 30, 2007	Database Update	18 Mb	ZIP/RNEF XML
Protein annotation and interactions from Entrez Gene (NCBI). Adds more than 18,000 Binding and over 800 PromoterBinding interactions to ResNet 5. Contains interaction data from BIND, HPRD and BioGRID. Depending on your computer the import of this file may take several hours. Please plan your time accordingly.
Hippocampal Signaling Pathway *	Dec 20, 2005	Database Update	23 Kb	ZIP/RNEF XML
File adds 1789 relations found by Maayan et al 2005.
A map of human cancer signaling *	Dec 30, 2007	Database Update	71 Kb	ZIP/RNEF XML
File adds 5089 relations curated by Cui et al 2007
Towards Human Proteome *	Dec 20, 2005	Database Update	130 Kb	ZIP/RNEF XML
File adds 6727 Binding relations. The relations have been found by Rual et al 2005 in Y2H screen.
Large-scale mapping of human protein-protein interactions by mass spectrometry *	Jul 28, 2007	Database Update	216 Kb	ZIP/RNEF XML
File contains 6545 Binding relations. The relations were found by Ewing et al in 2007.
A protein-protein interaction network for human inherited ataxias *	Aug 13, 2007	Database Update	98 Kb	ZIP/RNEF XML
File contains 6,972 Binding relations identified by Lim et al in 2006
A human protein-protein interaction network: a resource for annotating the proteome *	Oct 7, 2007	Database Update	88 Kb	ZIP/RNEF XML
Contains 5841 interactions for 1876 human proteins measured in Y2H screen by Stelzl et al, 2005.
Genetic association database (NIA) *	May 20, 2007	Database Update	8 Mb	ZIP/RNEF XML
Import 32,022 Regulation relations between protein and disease symbolizing genetic association from Genetic association database: http://geneticassociationdb.nih.gov
Human host-pathogen interactions *	Apr 14, 2008	Database Update	6 Mb	ZIP/RNEF XML
Contains 5160 interactions from Entrez Gene between human and pathogen proteins including 3677 intractions with HIV proteins. Also contains 9724 Binding of human proteins to pathogen proteins from Dyer et al. 2008
Cow (Bos taurus) protein annotation *	Aug 25, 2007	Database Update	6 Mb	ZIP/RNEF XML
After the import into ResNet5 database updates 16,452 proteins with annotation for Bos taurus and adds 12,785 new proteins.
Zebrafish protein annotation *	Sep 2, 2008	Database Update	7 Mb	ZIP/RNEF XML
After the import into ResNet5 database updates 13,930 proteins with annotation for Danio rerio and adds 34,338 new proteins.
Small Molecule Annotation *	Dec 27, 2006	Database Update	3 Mb	ZIP/Text
Plaintext file annotates Small molecules in ResNet database. RNEF XML file adds small molecule classification to ResNet database.
Microarray ID Annotation *	Jan 16, 2006	Database Update	3 Mb	ZIP/RNEF XML
Annotates proteins with Microarray Ids in ResNet database. Fixes application crashing during Select All operation in Expression viewer.

Plant Optional Updates

Title	Date	Type	Size	File type
Plants Co-occurence relations *	Jan 15, 2007	Database Update	145 Mb	ZIP/RNEF XML
Adds more than 300,000 co-occurrence facts to the Plant database. Co-occurrence fact symbolizes that two entities were mentioned in one sentence.
Rice protein annotation *	May 13, 2007	Database Update	2 Mb	ZIP/RNEF XML
Contains annotation for 29,063 rice proteins. Annotates 11,768 Arabidopsis proteins with annotation from rice orthologs and adds 17,295 new proteins to Plant 1.0 database. This file is required when using the rice microarray map files.
Protein cell localization for Plant 1.0 *	Jan 28, 2008	Database Update	130 Kb	ZIP/Text
Annotates 15700 proteins with cell localization in Plant 1.0 database

Yeast Optional Updates

Title	Date	Type	Size	File type
Yeast Phosphorylation Map *	Sep 11, 2008	Database Update	101 Kb	ZIP/RNEF XML
File adds 4152 ProtModification relations with ModificationType \"phosphorylation\". The relations have been found by Ptacek et all.
Yeast Protein Annotation by Concentration and Localization *	Sep 11, 2008	Database Update	85 Kb	ZIP/Text
This update adds annotations to the proteins in the Yeast database with the following attributes: 1. Cell Localization, based on Huh, W. K. et al, 2003. 2. Molecules per cell, based on Ghaemmaghami et al, 2003.
Yeast Microarray ID Annotation *	May 16, 2005	Database Update	16 Kb	ZIP/Text
Annotates Functional class entities with Microarray IDs.
High-Quality Binary Protein Interaction Map of the Yeast Interactome Network *	Sep 12, 2008	Database Update	33 Kb	ZIP/RNEF XML
This update adds 894 new Binding interactions to Yeast-3 database measured by Yu et al, 2008.

Mapfiles

Installation instructions for GenBank mapfile:

Unzip the file and close Pathway Studio.
Replace the file with the same name located in the Pathway Studio installation directory. Usually it is in ..\Program Files\Ariadne Genomics\PathwayStudio5\Mapfiles\
Delete the "GenBankMap.map" if it is present in the directory
Restart the software and import your gene list. Please wait for about 5-20 minutes to allow software rebuilding the "GenBankMap.map" file for the first time. After that you will be able to import many more genes from your list of GenBank identifiers.

Installation instructions for Microarray chip mapfiles:

Unzip the file and close Pathway Studio.
Add the file to the ExpressionChips\Organism folder in the Pathway Studio installation directory. Usually it is in ..\Program Files\Ariadne Genomics\PathwayStudio5\ExpressionChips\ . Choose sub-folder that is appropriate for the organism.
Start importing your expression experiment in Generic format. Choose Microarray ID as a Mapping attribute on the second page of the Expression import wizard. Added mapfiles will appear on the last page of the wizard.

Installation instructions for IPI mapfile:

Unzip the file and close Pathway Studio.
Copy the file into the Pathway Studio installation directory. Usually it is in ..\Program Files\Ariadne Genomics\PathwayStudio5\Mapfiles\
Start importing your expression experiment in Generic format. Choose IPI ID as a Mapping attribute on the second page of the Expression import wizard. Added mapfiles will appear on the last page of the wizard
If you do not have IPI ID in the list of attributes you have to declare IPI ID attribute by opening Edit properties dialog for any protein in the database and pressing the button Declare new property. Edit properties dialog can be opened by double-clicking on any protein in Pathway Studio.

Mapfiles

Title	Date	Type	Size	File type
Affymetrix Exon and Gene level arrays *	Apr 16, 2008	Mapfile	621 Kb	ZIP/Text
Mapfiles for Affymetrix MoEx-1_0, HuEx-1_0, RaEx-1_0, RaGene-1_0 chips. Only transcript level data from these chips should be imported into Pathway Studio.
Affymetrix Rhesus Macaque Genome Array *	Mar 3, 2008	Mapfile	269 Kb	ZIP/Text
Allows import of expression data from Affymetrix GeneChip® Rhesus Macaque Genome Array into mammalian Resnet database.
Affymetrix Chicken mapfile *	Mar 24, 2008	Mapfile	59 Kb	ZIP/Text
Allows import of Affymetrix Chicken genome array into mammalian Resnet database.
Affymetrix ZebraFish mapfile *	Sep 10, 2007	Mapfile	87 Kb	ZIP/Text
Allows import of Affymetrix ZebraFish genome array into mammalian Resnet database. Requires import of ZebraFish protein annotation prior to import of the expression data.
Mapfiles for Illumina chips *	Apr 16, 2007	Mapfile	2 Mb	ZIP/Text
Mapfiles for Illumina arrays: WG6, WGH v 2.0, HumanRef-8 v2, Mouse-6 v1.txt, Mouse-6 v1.1.txt, MouseRef-8 v1.1, Human-6 v1, Human-6 v2,MouseRef-8 v1,RatRef-12 v1, HumanRef-8 v1.
Agilent mapfiles *	Aug 15, 2007	Mapfile	356 Kb	ZIP/Text
Mapfiles for Agilent arrays:Mouse (V2) G4121B, Whole Mouse Genome G4122F.
Mapfile for NSF rice 2 20K and 3 45K chips *	May 13, 2007	Mapfile	278 Kb	ZIP/Text
Contains mapping of NSF probe IDs to rice Entrez Gene IDs. The file support import of experimtal data generated using NSF microarray chips into ResNet Plants database. Requires importing the Rice protein annotation update file to enable the expression data import.
Dog mapfile *	Aug 22, 2007	Mapfile	181 Kb	ZIP/Text
To import gene expression data from Canine Genome 2.0 Array into Dog database.
Dog-Human mapfile	Aug 22, 2007	Mapfile	181 Kb	ZIP/Text
To import expression data from Canine Genome 2.0 Array into ResNet Mammal database.
C.Elegans-Human mapfile *	Aug 15, 2007	Mapfile	40 Kb	ZIP/Text
To import expression data from Affymetrix C-elegans chip into ResNet Mammal database.
IPImapfile.zip *	Nov 20, 2007	Mapfile	1002 Kb	ZIP/Text
Contains mapping of 135,874 IPI IDs to proteins in mammalian Resnet 5 database.

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Database Updates

How to Import Update Files

Mammalian Quarterly Updates

Title

Date

Type

Size

File type

Public datasets in RNEF XML format for mammal database

Title

Date

Type

Size

File type

Plant Optional Updates

Title

Date

Type

Size

File type

Yeast Optional Updates

Title

Date

Type

Size

File type

Mapfiles

Installation instructions for GenBank mapfile:

Installation instructions for Microarray chip mapfiles:

Installation instructions for IPI mapfile:

Mapfiles

Title

Date

Type

Size

File type