PubChemSR - Download

* Installation: No installation is needed. Unzip the above file and just run PubChemSR.exe
* Fields Update: The "Fields Update" menu at Tools menu keeps the available fields list up-to-date. If you keep experiencing errors in retrieving data, try 'Fields Update' first and do the search again. If the problem persists, please send a email to the developer (juhur @ umich . edu) with detailed description of your problem.

* Structure search: Structure search is available again in the newest version (v3.5.2). Using 'WEB' button is still available: from the result pages, change the display to "UI List", then send to 'Text" for the list of UIDs. This list can be copy & pasted into the "Bulk Download" section.
* OS requirement: PubChemSR runs only on Microsoft windows based machines.

V 3.5.2 (10/19/2010)

PubChemSR homepage moved to new server (http://cheminfov.informatics.indiana.edu/PubChemSR/)

V 3.5.1 (10/15/2010)

Bugfix: BatchSearch failure.

V 3.5.0 (02/28/2009)

Enhancement: Automatic check up can be disabled/enabled.
Bugfix: Structure search is now available again.

V 3.4.3 (02/27/2009)

Enhancement: Figure sub directories (cis/sid) are further checked for their existence.
Enhancement: Directory name now has date and time for BatchSearch
Bugfix: Opening two BatchSearch crashes the PubChemSR.

V 3.4.2 (10/06/2008)

Update) BioAssay retriever has been modified to accommodate the change in the NCBI querying system.
Update) Field data has been updated.
Update) Default for the number of document per retrieval (internal not the total number) is now set t0 100. (previously it was 50)
New) New version check of PubChemSR has been added.

V 3.4.1 (05/06/2008)

Field data has been updated.
BioAssay data retrieval has been modified according to the changes in the NCBI's webpages

V 3.4.0 (01/08/2008)

Actual bioactivity data is now automatically retrieved and merged to the selected field output.
URL Analyzer updated to handle non-structure search result pages
Maximum number of records for URL Analyzer can be specified
Bug fix for previewing of records more than the specified max-preview number
New manual file
Email address has changed

V 3.3.0 (11/21/2007)

Bioassay Retriever has been added.

Available through mouse right-click from BioAssay search result (Main window) or Menu/Tools/BioAssayRetriever

V 3.2.3 (11/10/2007)

New homepage and URLs for contact
New: addition of new threshold of the number of records of list-type data like SynonymList

You can now set to 1 to get only the first synonym.

Bug-fix: 'Abort' in 'BatchSearch' mode
Bug-fix: When query returned no result from NCBI server
Bug-fix: Wrong path error during image display

V 3.2.0 (09/24/2007)

New: In BatchSearch mode, results from multiple queries can be merged (default).

(Option: "Merge result into single files")
Ex) Getting only ONE 'canoonicalSmiles' for the following queries

1) Select only CanonicalSmile filed in 'Database Field'
2) Enter your queries. (Most of the typos can be tolerated)
3) Make sure to check 'Merge' option with 'Only the first 1'
4) Click 'Process'
5) When completed, click 'Open directory' button to see the results.

V 3.0.0 (08/05/2007)

New: BatchSearch for multiple query has been added.
Bug-fix: Minor bugs

V 2.0.2 (07/29/2007)

Update: Structure search has been updated according to NCBI's change.

V 2.0.1 (06/13/2007)

Update: Modification of structure search according to the changes at NCBI site.

V 2.0.0 (05/25/2007)

New: Structure search has been added
New: Page jump has been added
Bug-fix: A few bugs have been fixed
System: Migration from VB .Net 2003 to VB .Net 2005 (.Net Framework v2.0)

V 1.9.3 (10/18/2006)

V 1.9.2 (09/12/2006)

V 1.9.1 (09/8/2006)

V 1.8.5 (08/31/2006)

"Microsoft.Office.Interop.Excel.dll" file which is needed for some machines.

V 1.8.4 (08/26/2006)

V 1.8.0 (08/19/2006)

V 1.7.2 (06/29/2006)

V 1.7.1 (06/24/2006)

V 1.7.0 (06/23/2006)

New: Fully implemented structure search.
Two different modes of structure drawing are now supported.
Toggling options for structure preview selection are supported.
Preference menu has been renovated.
A bug in preference menu (default) has been fixed.

V 1.6.1 (06/05/2006)

Added ChemBioGrid logo
JME structure editor has been incorporated. But similarity searching is still not available.
GUI of the PubChrmSR has been significantly modified.

V 1.6.0 (04/26/2006)

V 1.5.0 (02/26/2006)

Structure previews of searched chemical compounds.
Upgraded UID checking feature for duplicated UIDs in 'Mass Download' section.
UID checking function has been upgraded to correctly handle Duplicated UIDs in the ‘Mass Download’.
The number of records per page has now been set to 10. This can’t be changed through preference anymore.
The name of manual file has been changed to ‘PubChemSR.pdf’ from ‘PubChemSR_Manual.pdf’.
Minor bugs have been fixed including wrong page number.

V 1.3.3 (02/02/2006)

Initial Logo screen is included
Default file extension (.txt) is supported in Open/Save file
Bug (when ./end directory is missing) has been fixed
Bug of wrong list of PC Compounds target fields has been fixed

V 1.3.2 (01/31/2006)

Custumizable preferences have been added. (FULLY working)
Spelling check for entered search terms has been improved.
Retrived data can be directly transferred to MS Excel
And many other minor improvement inside the program

V 1.3.1 (01/29/2006)

Custumizable preferences has been added. (Not fully working)
Spelling check for entered search terms has been implemented.

V 1.2.0 (11/21/2005)

Updating field list has been added.

V 1.1.0 (11/19/2005)

Large numbers of UIDs are split into smaller sets in order to avoid system half.
Name of the PubChem database is checked when a UID file is used.

UID list file should contain one the following three lines

“#cid” for Compound
“#sid” for Substance
“#aid” for BioAssay not including the double-quotation marks “”

Search button has been added. This button will open the PubChem website and performs search over there. This is especially useful when the search has resulted in a tremendous number. (ex) all[filter] as search term which will retrieve all the records in the PubChem databases)
Output file error is handled and displayed.
Download percentage is added. You can now see the progress in the status bar at the bottle of the program.
Tooltips (Balloon help) are now implemented to briefly introduce each databases and UIDs
Internal process orders have been reorganized. (ex, output file selection comes first)

V 1.0.0 (11/17/2005)

Initial release