User contributions
From irefindex
- 14:38, 10 May 2011 diff hist +392 iRefScape 0.8 Added compatibility table and remarks.
- 14:35, 10 May 2011 diff hist +118 iRefScape 1.0 Fixed some version numbers; added a link to the latest release page.
- 14:34, 10 May 2011 diff hist +354 iRefScape 0.9 Added compatibility table and remarks.
- 14:26, 10 May 2011 diff hist +131 iRefScape 1.0 Tidied up. Moved away from x-suffixed version numbers.
- 13:31, 9 May 2011 diff hist -679 iRefScape Test Cases 1.0 →Test case name: geneSymbol 1: Tried to test this.
- 11:30, 9 May 2011 diff hist 0 m Donaldson Group →The Donaldson Group at the Biotechnology Centre of Oslo: Attempt to move the share button.
- 11:25, 9 May 2011 diff hist -1 m iRefIndex Attempt to move the share button.
- 17:11, 3 May 2011 diff hist +15 iRefIndex Added "like" button.
- 16:56, 3 May 2011 diff hist +13 m Donaldson Group Moved the "like" button down since it now isn't being floated.
- 14:49, 3 May 2011 diff hist 0 m Donaldson Group →The Donaldson Group at the Biotechnology Centre of Oslo: Move the button.
- 14:40, 3 May 2011 diff hist 0 m Donaldson Group Experiment with a smaller "like" box, moved to the top of the page.
- 14:05, 3 May 2011 diff hist +207 N irefindex:Privacy policy Added privacy policy.
- 13:23, 3 May 2011 diff hist -80 Donaldson Group →Contact: Try out the Facebook like button.
- 11:27, 3 May 2011 diff hist +84 m Donaldson Group Added a comment to get bookmarking icons to appear.
- 11:06, 3 May 2011 diff hist +15 m Donaldson Group Test the ShareThis extension.
- 12:34, 2 May 2011 diff hist +505 iRefScape Test Cases 1.0 →Test case name: geneID 1: Added note about the isoform search.
- 16:15, 29 April 2011 diff hist 0 m iRefScape Test Cases 1.0 →Test case name: UniProt_ID 1: Minor formatting change.
- 16:14, 29 April 2011 diff hist -337 iRefScape Test Cases 1.0 →Test case name: geneID 1: Updated for 1.0.
- 13:40, 28 April 2011 diff hist -52 iRefScape Test Cases 1.0 →Test case name: UniProt_ID 1: Reviewed the test.
- 13:39, 27 April 2011 diff hist +42 N iRefScape A redirect to the latest stable version of the page.
- 16:32, 19 April 2011 diff hist +140 MediaWiki:Sidebar Added PSICQUIC and PSISCORE usage links.
- 11:42, 8 April 2011 diff hist +2,552 iRefIndex Output and Statistics →PSI-MI Controlled Vocabulary Mapping: Added Wiki page construction notes.
- 12:50, 7 April 2011 diff hist -1 Mapping of terms to MI term ids - iRefIndex 8.0 Fixed numbered list. current
- 12:50, 7 April 2011 diff hist -3 m Mapping of terms to MI term ids - iRefIndex 6.0 Changed numbered list. current
- 12:49, 7 April 2011 diff hist -363 Mapping of terms to MI term ids - iRefIndex 8.0 →Interaction Detection Method: Edited according to the MITAB data.
- 12:42, 7 April 2011 diff hist -33 Mapping of terms to MI term ids - iRefIndex 8.0 →Interaction Type: Edits based on looking at the MITAB data.
- 12:36, 7 April 2011 diff hist +26,878 N Mapping of terms to MI term ids - iRefIndex 8.0 Added initial transcription of the spreadsheet.
- 14:10, 6 April 2011 diff hist 0 MediaWiki:Sidebar Use asclepius for now.
- 14:10, 6 April 2011 diff hist +44 MediaWiki:Sidebar Try with absolute URLs.
- 14:09, 6 April 2011 diff hist +4 MediaWiki:Sidebar Try with relative URLs.
- 14:08, 6 April 2011 diff hist -32 MediaWiki:Sidebar Attempted to add links to other services, removing redundant links.
- 12:18, 5 April 2011 diff hist +21 PSICQUIC Web Services for iRefIndex Changed host name.
- 15:34, 30 March 2011 diff hist +107 PSICQUIC Web Services for iRefIndex Added PSISCORE URLs. Minor formatting changes.
- 10:52, 29 March 2011 diff hist -2 m Donaldson Group →Courses: Test edit.
- 09:45, 28 March 2011 diff hist +17 README MITAB2.6 for iRefIndex 8.0 →Column number: 15 (confidence): Fixed formatting.
- 17:08, 21 March 2011 diff hist +134 DrugBank MITAB2.6 File Format →Format Summary: Updated the taxonomy description and adjusted the formatting.
- 17:04, 21 March 2011 diff hist -232 Donaldson Group →Local Seminar Series: Removed specific seminar details and updated links.
- 16:51, 21 March 2011 diff hist -52 m Bioseminar Removed specific details of the seminars.
- 18:39, 17 March 2011 diff hist +606 iRefIndex MITAB2.6 Parser →Notes on the Populated Database: Added interaction RIG tables and some notes about interactor identifiers.
- 18:31, 17 March 2011 diff hist 0 N File:mitab-2011-03-17.tar.bz2 current
- 18:30, 17 March 2011 diff hist 0 iRefIndex MITAB2.6 Parser →Obtaining the MITAB Parser: Added new snapshot.
- 15:44, 11 March 2011 diff hist +3 README MITAB2.6 for iRefIndex 8.0 →Column number: 52 (imex_id): Fixed example.
- 14:26, 23 February 2011 diff hist +8 iRefWeb LinkOut Generator →Obtaining the Generator: Fixed filename. current
- 14:25, 23 February 2011 diff hist +57 N File:iRefWeb-LinkOut-2011-02-23.tar.bz2 The 2011-02-23 snapshot of the iRefWeb LinkOut generator. current
- 14:24, 23 February 2011 diff hist -9 iRefWeb LinkOut Generator →Obtaining the Generator: Changed filename.
- 14:19, 23 February 2011 diff hist +1,328 N iRefWeb LinkOut Generator Added a page about iRefWeb and LinkOut.
- 14:13, 23 February 2011 diff hist -335 iRefIndex MITAB2.6 Parser →Obtaining the MITAB Parser: Reference an uploaded file.
- 14:08, 23 February 2011 diff hist +54 N File:mitab-2011-02-23.tar.bz2 The 2011-02-23 snapshot of the iRefIndex MITAB parser. current
- 17:52, 22 February 2011 diff hist +1,399 DrugBank MITAB2.6 File Format Changed DrugBank to drugbank and InChIKey to inchikey for general consistency. Added the remaining columns.
- 13:47, 15 February 2011 diff hist -71 m iRefIndex Videos Reverted edits by PaulBoddie (Talk) to last revision by Ian.donaldson current
- 13:23, 15 February 2011 diff hist +71 iRefIndex Videos Test with MediawikiPlayer extension.
- 13:25, 11 February 2011 diff hist +113 DrugBank MITAB2.6 File Format →Format Summary: Added biological role A.
- 14:10, 8 February 2011 diff hist +1,298 DrugBank MITAB2.6 File Format →Format Summary: Added columns.
- 18:25, 31 January 2011 diff hist +203 DrugBank MITAB2.6 File Format →Format Summary: Fixed protein alias source, added an example column.
- 17:47, 31 January 2011 diff hist +1,111 DrugBank MITAB2.6 File Format →Format Summary: Added sources, more fields.
- 19:05, 27 January 2011 diff hist +672 DrugBank MITAB2.6 File Format Added field descriptions.
- 16:08, 27 January 2011 diff hist +1,033 N DrugBank MITAB2.6 File Format Added initial description.
- 18:20, 17 January 2011 diff hist +129 iRefIndex Maintenance Added some resources of peripheral interest.
- 16:37, 21 December 2010 diff hist +104 iRefIndex Build Process →Recreate SEGUID: Added note.
- 14:41, 21 December 2010 diff hist +493 iRefIndex Build Process →Running BioPSI_Suplimenter (continued): Added SEGUID Manipulator.
- 17:13, 1 December 2010 diff hist +89 iRefIndex Build Process →Running BioPSI_Suplimenter (continued): Added Canonical_Mapper.
- 17:04, 1 December 2010 diff hist -5 m iRefIndex Build Process →Running BioPSI_Suplimenter: Change .jar path.
- 10:07, 30 November 2010 diff hist +128 iRefIndex Output and Statistics →Running PSI_MI_TAB_Maker: Added taxid2name statements.
- 16:46, 29 November 2010 diff hist +97 iRefIndex Release Process →Testing the Output: Added link to new page.
- 16:50, 11 November 2010 diff hist +111 iRefIndex Build Process →Running BioPSI_Suplimenter (continued): Extended workaround.
- 15:42, 5 November 2010 diff hist +936 iRefIndex Build Process →ROG_ass + RIG_fill+ make Cy: Added Eutils-related notes.
- 17:06, 2 November 2010 diff hist +1 iRefIndex MITAB2.6 Parser →Prerequisites: Updated versions.
- 15:00, 28 October 2010 diff hist +1,289 iRefIndex Build Process →Validating the Results from iRef_PSI_XML2RDBMS: Added notes about problems with the parsed data.
- 12:37, 28 October 2010 diff hist +268 iRefIndex Build Process →Validating the Results from iRef_PSI_XML2RDBMS: Added source2object queries.
- 13:44, 27 October 2010 diff hist +192 README iRefIndex expanded MITAB proposal Added deprecation note. current
- 13:35, 27 October 2010 diff hist +27 m iRefIndex MITAB2.6 Parser Minor formatting changes.
- 13:33, 27 October 2010 diff hist +254 iRefIndex MITAB2.5 Parser Added status note.
- 13:29, 27 October 2010 diff hist 0 m README iRefIndex MITAB experiment proposal for 7.0 moved README MITAB experiment proposal for iRefIndex 7.0 to README iRefIndex MITAB experiment proposal for 7.0: Fixed the name of the page. current
- 13:29, 27 October 2010 diff hist +64 N README MITAB experiment proposal for iRefIndex 7.0 moved README MITAB experiment proposal for iRefIndex 7.0 to README iRefIndex MITAB experiment proposal for 7.0: Fixed the name of the page. current
- 13:28, 27 October 2010 diff hist 0 m README iRefIndex MITAB experiment proposal for 7.0 moved README iRefIndex experiment MITAB 7.0 to README MITAB experiment proposal for iRefIndex 7.0: The page describes an obsolete format.
- 13:28, 27 October 2010 diff hist +64 N README iRefIndex experiment MITAB 7.0 moved README iRefIndex experiment MITAB 7.0 to README MITAB experiment proposal for iRefIndex 7.0: The page describes an obsolete format. current
- 13:27, 27 October 2010 diff hist +435 README iRefIndex MITAB experiment proposal for 7.0 Added deprecation note.
- 15:44, 25 October 2010 diff hist +13 README MITAB2.6 for iRefIndex 7.0 →Column number: 1 (uidA): Minor formatting edit. current
- 15:42, 25 October 2010 diff hist -427 iRefIndex MITAB2.6 Parser Updated the description of the software.
- 15:24, 25 October 2010 diff hist +12 iRefIndex Build Process →Validating the Results from iRef_PSI_XML2RDBMS: Added missing name columns to certain queries.
- 15:14, 21 October 2010 diff hist +1,016 iRefIndex Build Process →Validating the Results from iRef_PSI_XML2RDBMS: Added undefined value queries.
- 12:20, 19 October 2010 diff hist +238 README iRefIndex MITAB2.6 proposal for 7.0 Added status note, updated release details. current
- 11:55, 19 October 2010 diff hist 0 m README iRefIndex MITAB2.6 proposal for 7.0 moved README iRefIndex MITAB2.6 7.0 to README iRefIndex MITAB2.6 proposal for 7.0: This is no longer relevant.
- 11:55, 19 October 2010 diff hist +56 N README iRefIndex MITAB2.6 7.0 moved README iRefIndex MITAB2.6 7.0 to README iRefIndex MITAB2.6 proposal for 7.0: This is no longer relevant. current
- 17:38, 18 October 2010 diff hist +641 README MITAB2.6 for iRefIndex 7.0 Various formatting and wording changes and fixes.
- 14:31, 15 October 2010 diff hist +457 iRefIndex Development →Defining the Database Identifier: Fixed the origin of identifiers.
- 13:24, 15 October 2010 diff hist +984 iRefIndex Development Added database identifier definition.
- 19:00, 14 October 2010 diff hist +77 README MITAB2.6 for iRefIndex 7.0 →Representation of interactions: Fixed formatting, list numbering, some wording.
- 18:37, 14 October 2010 diff hist +565 iRefIndex Build Process →Known Issues: Added BioGRID fix.
- 14:53, 14 October 2010 diff hist -271 iRefIndex Build Process →Known Issues: Switched back to the PSI-MI XML 2.5 version of BioGRID.
- 14:52, 14 October 2010 diff hist +5 Sources iRefIndex 8.0 →Interaction related resources: Fixed BioGRID reference.
- 13:27, 14 October 2010 diff hist -3 iRefIndex Build Process →Running the Program: Changed the execution method.
- 13:10, 14 October 2010 diff hist +497 iRefIndex Build Process →Known Issues: Updated the issues with observations from iRefIndex 8.0.
- 12:23, 14 October 2010 diff hist +161 iRefIndex Build Process →Running iRef_PSI_XML2RDBMS: Changed the formatting, added new data sources, changed source removal (adding, not removing # characters).
- 14:10, 13 October 2010 diff hist +161 iRefIndex Build Process →MIPS: Introduced a separate MPACT directory.
- 14:02, 13 October 2010 diff hist 0 iRefIndex Build Process Changed BioGrid to BioGRID.
- 10:22, 13 October 2010 diff hist +364 iRefIndex Build Process →Creating the Database: Added more restrictive grant statements.
- 17:03, 12 October 2010 diff hist +8 m iRefIndex Build Process →Validating the Results from StaxPSIXML: Changed the module name.
- 17:01, 12 October 2010 diff hist +2,376 iRefIndex Development →Adapting an Existing Mapper File: Added notes about different data origins.
- 16:37, 12 October 2010 diff hist +18,772 iRefIndex Development →Evaluating the Data: Updated the data structure output. Added MatrixDB.
- 14:37, 11 October 2010 diff hist +4,929 iRefIndex Development Added notes about adapting mapper files.
- 11:33, 11 October 2010 diff hist -1,991 iRefIndex Development →Reviewing Mapper Files: Updated output.
- 14:11, 8 October 2010 diff hist +91 iRefIndex Development →Evaluating the Data: Added InnateDB observations.
- 18:11, 7 October 2010 diff hist +8,416 iRefIndex Development →Adding Sources to iRefIndex: Updated the script invocation and added an explanation of the output.
- 16:10, 1 October 2010 diff hist +5,155 iRefIndex Development →Adding Sources to iRefIndex: Added description of XML element path analysis.
- 14:11, 1 October 2010 diff hist +319 iRefIndex Build Process →Running StaxPSIXML: Introduced iRef_PSI_XML2RDBMS references and described the convenience script.
- 14:01, 1 October 2010 diff hist -55 iRefIndex Build Process →Building StaxPSIXML: Introduced references to iRef_PSI_XML2RDBMS.
- 16:29, 30 September 2010 diff hist 0 m iRefIndex Build Process →BioGrid: Capitalisation changes.
- 14:04, 30 September 2010 diff hist +643 Gene Ontology similarity measurement Added concept comparison notes.
- 13:22, 30 September 2010 diff hist +182 iRefIndex Build Process →Clone seguid: Added a note about updating from a newer seguidannotation file. Modified the wording.
- 17:06, 28 September 2010 diff hist +3,367 N Gene Ontology similarity measurement Some initial notes.
- 16:21, 28 September 2010 diff hist +23 m DiG: Disease groups/Bioscape Notes Added category. current
- 16:15, 24 September 2010 diff hist +16 m iRefIndex Build Process →Running BioPSI_Suplimenter: Qualify the initial statement.
- 16:14, 24 September 2010 diff hist +195 iRefIndex Build Process →Manual loading of data: Added maintenance note.
- 15:54, 23 September 2010 diff hist +19 Sources iRefIndex 8.0 Added InnateDB details, removed OPHID.
- 15:54, 23 September 2010 diff hist +482 iRefIndex Build Process →Manual Downloads: Added InnateDB details.
- 15:32, 23 September 2010 diff hist +72 Sources iRefIndex 8.0 Updated MINT, Intact (probably unchanged, timestamp adjusted), NCBI resources.
- 16:08, 21 September 2010 diff hist +539 iRefIndex Build Process →Running SaxValidator: Added xmllint notes.
- 13:08, 21 September 2010 diff hist -16 iRefIndex Build Process →Running BioPSI_Suplimenter: Tidied the link to the previous section.
- 12:56, 21 September 2010 diff hist -16 Sources iRefIndex 8.0 →Sequence related resources: Changed SEGUID details, although the actual contents of seguidannotation is unchanged from the previous release.
- 11:04, 21 September 2010 diff hist +99 iRefIndex Build Process Updated the sources link and added a note about SEGUID.
- 16:55, 20 September 2010 diff hist +111 Sources iRefIndex 8.0 →Sequence related resources: Updated UniProt details.
- 16:16, 20 September 2010 diff hist +987 iRefIndex Build Process Added Ant installation information.
- 15:57, 20 September 2010 diff hist -99 iRefIndex Build Process Tidied formatting.
- 15:51, 20 September 2010 diff hist -43 iRefIndex Build Process →Building FTPtransfer: Tidied formatting.
- 11:39, 15 September 2010 diff hist +167 Sources iRefIndex 8.0 →Interaction related resources: Updated DIP, added MatrixDB, MPIDB, InnateDB details.
- 08:55, 15 September 2010 diff hist -71 m Bioinformatics course Removed weird "skype highlighting" text.
- 16:49, 14 September 2010 diff hist -4 Sources iRefIndex 8.0 →Interaction related resources: Updated I2D details.
- 16:08, 14 September 2010 diff hist +1 Sources iRefIndex 8.0 →Interaction related resources: Updated HPRD, removing the trailing / which upsets their site.
- 12:54, 14 September 2010 diff hist +10 Sources iRefIndex 8.0 →Interaction related resources: Tidied, fixed and confirmed BIND Translation details. Updated BioGRID details.
- 12:00, 14 September 2010 diff hist +47 iRefIndex Build Process →BIND Translation: Updated the download information.
- 09:32, 6 September 2010 diff hist -71 m Bioinformatics course Removed weird "skype highlighting" text.
- 13:46, 23 August 2010 diff hist -11 iRefIndex →Contact: Fixed link to new Biotek site.
- 14:31, 5 August 2010 diff hist +3 m README MITAB2.6 for iRefIndex 7.0 →Understanding the iRefIndex MITAB format: Minor fixes and formatting changes.
- 16:58, 15 July 2010 diff hist -356 Bioseminar Updated the page to give details of the new arrangements.
- 16:48, 15 July 2010 diff hist +5,192 Bioscape Result Assessment Added notes about disambiguation using unambiguous/reliable gene mentions. current
- 13:49, 14 July 2010 diff hist -92 m Bioscape Issues and Tasks Moved note to a separate page. current
- 13:48, 14 July 2010 diff hist -92 m Bioscape Development Moved note to a separate page. current
- 13:48, 14 July 2010 diff hist +22 m Displaying Bioscape Search Results Added status note. current
- 13:47, 14 July 2010 diff hist +22 m Bioscape Web Resources Added status note. current
- 13:47, 14 July 2010 diff hist +22 m Bioscape Result Assessment Added status note.
- 13:46, 14 July 2010 diff hist +22 m Bioscape Searching Techniques Added status note. current
- 13:46, 14 July 2010 diff hist +22 m Bioscape Searching Added status note. current
- 13:45, 14 July 2010 diff hist +22 m Bioscape Tokenisation Added status note. current
- 13:45, 14 July 2010 diff hist +71 Bioscape Indexing Added status note. Clarified the status of the indexing solutions used in Bioscape. current
- 13:44, 14 July 2010 diff hist +22 m Bioscape Scoring Techniques Added status note. current
- 13:43, 14 July 2010 diff hist -92 m Bioscape Methods Moved note to a separate page. current
- 13:42, 14 July 2010 diff hist +22 m Bioscape Data Types Added status note. current
- 13:41, 14 July 2010 diff hist +141 Supported Data Sources Added status note, changed note appearances, added GeneRIF. current
- 13:39, 14 July 2010 diff hist +22 m Bioscape Data Sources Added status note. current
- 13:39, 14 July 2010 diff hist -92 m Bioscape Distribution Moved note to a separate page. current
- 13:38, 14 July 2010 diff hist +22 m Bioscape Workflow Added status note. current
- 13:38, 14 July 2010 diff hist +22 m Bioscape Configuration Added status note. current
- 13:37, 14 July 2010 diff hist -145 Bioscape Dependencies Moved note to a separate page. Removed Lucene from the dependencies. current
- 13:36, 14 July 2010 diff hist -92 m Bioscape Installation Moved note to a separate page. current
- 13:36, 14 July 2010 diff hist -92 m Bioscape Manual Moved note to a separate page. current
- 13:35, 14 July 2010 diff hist +103 N Bioscape Status Added a common note for inclusion in other pages. current
- 15:34, 9 July 2010 diff hist +6,161 N iRefIndex MITAB2.6 Parser Attempted to make a page corresponding to the revised MITAB format.
- 16:17, 8 July 2010 diff hist +485 README iRefIndex MITAB2.6 proposal for 7.0 →Understanding the iRefIndex MITAB format: Added some notes about finding different group sizes.
- 15:27, 8 July 2010 diff hist +2,195 README iRefIndex MITAB2.6 proposal for 7.0 →Understanding the iRefIndex MITAB format: Introduced sections. Added a description of the canonical interaction information.
- 18:12, 7 July 2010 diff hist -151 README iRefIndex MITAB2.6 proposal for 7.0 →Description: Updated version references.
- 18:10, 7 July 2010 diff hist +207 README iRefIndex MITAB2.6 proposal for 7.0 →Understanding the iRefIndex MITAB format: Updated the table.
- 17:44, 7 July 2010 diff hist -2,717 README iRefIndex MITAB2.6 proposal for 7.0 Removed columns 41 and 42. Renumbered the columns and references to columns.
- 17:03, 7 July 2010 diff hist -1,168 README iRefIndex MITAB2.6 proposal for 7.0 Removed columns 47 (replacing 35), 53.
- 16:58, 7 July 2010 diff hist +231 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 52 (numParticipants): Added a description of how this value can be different from the number of distinct interactors.
- 16:56, 7 July 2010 diff hist -54 m README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 51 (edgetype): Removed notes.
- 16:54, 7 July 2010 diff hist -35 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 44 (entrezGeneIds_B): Replaced with irogB.
- 16:54, 7 July 2010 diff hist -115 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 43 (entrezGeneIds_A): Replaced with irogA.
- 16:48, 7 July 2010 diff hist +14 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 39 (Final_ROGID_A): Column change.
- 16:47, 7 July 2010 diff hist +4 m README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 36 (Negative): Added horizontal rule.
- 16:46, 7 July 2010 diff hist -278 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 34 (Checksum_B): Replaced with content from After_C13N_ROGID_B in column 42.
- 16:44, 7 July 2010 diff hist +2,196 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 33 (Checksum_A): Replaced the content with the After_ROGID_A content previously in column 41.
- 16:30, 7 July 2010 diff hist -1 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 1 (uidA): Fixed column type.
- 16:30, 7 July 2010 diff hist -29 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 2 (uidB): Changed the example to reflect the updated nature of the field.
- 16:29, 7 July 2010 diff hist -795 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 1 (uidA): Changed the nature of the identifier, as discussed.
- 16:27, 7 July 2010 diff hist -3 README iRefIndex MITAB2.6 proposal for 7.0 →Understanding the iRefIndex MITAB format: Fixes in wording, formatting.
- 14:57, 6 July 2010 diff hist -10 README iRefIndex MITAB2.6 proposal for 7.0 →Understanding the iRefIndex MITAB format: Fixed Final_ROGID names.
- 14:57, 6 July 2010 diff hist -5 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 40 (Final_C13N_ROGID_B): Fixed name, referenced column number.
- 14:56, 6 July 2010 diff hist -5 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 39 (Final_C13N_ROGID_A): Fixed name.
- 11:34, 5 July 2010 diff hist +33 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 11 (taxb): Fixed column type and description.
- 11:33, 5 July 2010 diff hist +33 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 10 (taxa): Fixed the column type and description.
- 11:18, 5 July 2010 diff hist -91 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 16 (expansion): Fixed internal link.
- 10:52, 5 July 2010 diff hist +90 README iRefIndex MITAB2.6 proposal for 7.0 →Understanding the iRefIndex MITAB format: Updated the columns in the table.
- 10:13, 5 July 2010 diff hist +15 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 41 (After_C13N_ROGID_A): Tidying, name and column updates.
- 10:03, 5 July 2010 diff hist -4 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 48 (C13N_rig): Tidied up naming.
- 10:01, 5 July 2010 diff hist 0 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 52 (numParticipants): Fixed edgetype column number.
- 10:00, 5 July 2010 diff hist +100 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 53 (interaction_name): Tidied up. Expanded the "to do" note.
- 08:35, 5 July 2010 diff hist -68 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 51 (edgetype): Fixed link to refer within the same document.
- 16:46, 2 July 2010 diff hist +226 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 37 (OriginalReferenceA): Added a note about the relationship between this column and the old altA column.
- 15:59, 2 July 2010 diff hist -129 m README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 46 (MappingScoreB): Removed Sabry's marker.
- 15:58, 2 July 2010 diff hist +34 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 45 (MappingScoreA): Merged Sabry's comment and tidied.
- 15:50, 2 July 2010 diff hist +202 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 43 (entrezGeneIds_A): Added a more complete change note.
- 14:53, 2 July 2010 diff hist +183 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 5 (aliasA): Minor formatting, wording changes.
- 14:36, 2 July 2010 diff hist -2 m README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 32 (Update_date): Removed empty lines.
- 14:35, 2 July 2010 diff hist -13 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 29 (Host_organism_taxid): Various wording, formatting changes.
- 14:32, 2 July 2010 diff hist +45 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 26 (Annotations_A): Minor formatting changes.
- 14:05, 2 July 2010 diff hist +35 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 16 (expansion): Minor formatting changes.
- 14:02, 2 July 2010 diff hist +7 m README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 23 (xrefs_A): Minor formatting change.
- 13:57, 2 July 2010 diff hist -54 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 19 (experimental_role_A): Merged Sabry's comment.
- 13:56, 2 July 2010 diff hist +1 m README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 18 (biological_role_B): Minor formatting change.
- 13:56, 2 July 2010 diff hist -43 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 17 (biological_role_A): Minor formatting changes. Merged Sabry's comment.
- 13:53, 2 July 2010 diff hist +1 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 13 (sourcedb): Minor naming change.
- 13:52, 2 July 2010 diff hist +2 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 14 (interactionIdentifier): Minor formatting, wording changes.
- 13:49, 2 July 2010 diff hist +133 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 14 (interactionIdentifier): Minor formatting, wording changes.
- 13:46, 2 July 2010 diff hist +25 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 9 (pmids): Minor formatting, capitalisation changes.
- 13:20, 2 July 2010 diff hist +60 README iRefIndex MITAB2.6 proposal for 7.0 →Column number: 10 (taxa): Formatting changes.
- 12:59, 2 July 2010 diff hist -2,536 README iRefIndex MITAB2.6 proposal for 7.0 Removed column name table entries which were redundant duplicates of the headings. Added a change note about the altA column. Fixed some column types.
- 18:52, 1 July 2010 diff hist -121 README iRefIndex MITAB2.6 proposal for 7.0 Added a canonical interactor row to the explanatory table, moving various columns into it. Propagated column names for #39 and #40. Formatting changes. Updated various column headings.
- 16:59, 1 July 2010 diff hist +54,037 N README iRefIndex MITAB2.6 proposal for 7.0 Formatted the note at the top, added the table from 7.0 explaining the columns, added a last updated "macro". Introduced change note formatting. Formatted various examples.
- 16:33, 1 July 2010 diff hist +260 Template:Note →Usage: Added note about method 1. current
- 16:28, 1 July 2010 diff hist -4 Template:Note →Method 1: Attempt to make the template actually work.
- 16:26, 1 July 2010 diff hist +2 Template:Note →Method 1: Attempt to make the template actually work.
- 16:17, 1 July 2010 diff hist +726 Template:Note Added support for a different label, hopefully.
- 16:06, 1 July 2010 diff hist +17 Template:Note Changed text appearance.
- 16:05, 1 July 2010 diff hist +17 Template:Warning Changed text appearance. current
- 15:41, 1 July 2010 diff hist +21 Template:Warning Edited to match the note template.
- 15:39, 1 July 2010 diff hist +57 Template:Note Added padding and border.
- 15:37, 1 July 2010 diff hist -42 Template:Note Changed the label depending on whether a parameter is supplied.
- 15:16, 1 July 2010 diff hist +3 Template:Warning Changed icon alignment.
- 15:09, 1 July 2010 diff hist +3 Template:Note Changed icon alignment.
- 13:32, 1 July 2010 diff hist 0 Template:Note Fixed usage.
- 13:16, 1 July 2010 diff hist +172 Template:Note Fixed template rule, adopting the warning template's rule.
- 13:13, 1 July 2010 diff hist +33 N File:Attention niels epting.svg Warning icon from MediaWiki 1.16. current
- 13:12, 1 July 2010 diff hist +33 N File:Attention niels epting-18px.svg.png Warning icon from MediaWiki 1.16. current
- 13:07, 1 July 2010 diff hist 0 Template:Warning Fixed usage.
- 12:52, 1 July 2010 diff hist 0 Template:Note →Usage: Fixed template usage.
- 09:59, 1 July 2010 diff hist -82 Bioinformatics course Switched to percentages. Removed weird "skype highlighting" text. Tidied whitespace. Fixed year.
- 14:46, 30 June 2010 diff hist +113 iRefIndex MITAB2.5 Parser Added a link to the format description.
- 11:59, 30 June 2010 diff hist +77 Donaldson Group Tidied the content. Updated the Bioseminar details.
- 13:39, 15 June 2010 diff hist +900 Bioscape Searching Techniques Added example involving collections/sequences.
- 12:58, 14 June 2010 diff hist 0 m iRefScape 0.8 Installation Minor notation changes.
- 16:02, 10 June 2010 diff hist +193 iRefScape 0.8 Installation →Manual Installation: Improved and extended the note.
- 10:59, 10 June 2010 diff hist 0 m iRefIndex Minor capitalisation and punctuation fixes.
- 10:56, 10 June 2010 diff hist +24 m iRefScape 0.8 Installation Added category.
- 10:32, 10 June 2010 diff hist +1 m iRefScape 0.8 Installation Minor capitalisation and punctuation fixes.
- 10:14, 10 June 2010 diff hist +461 iRefScape 0.8 Installation Various formatting and other changes/updates.
- 09:45, 9 June 2010 diff hist -134 m iRefScape 0.8 Formatting changes to tables.
- 14:43, 8 June 2010 diff hist +72 iRefScape 0.8 Modified headings. Moved images.
- 14:37, 8 June 2010 diff hist +284 iRefScape 0.8 →Advanced path-finding: Added new images.
- 14:37, 8 June 2010 diff hist +32 N File:iRefIndex-0.83-path-original.png The path highlighted in a graph. current
- 14:25, 8 June 2010 diff hist 0 File:iRefIndex-0.83-path.png uploaded a new version of "File:iRefIndex-0.83-path.png": A path highlighted in a graph. current
- 14:22, 8 June 2010 diff hist +30 N File:iRefIndex-0.83-path.png A path highlighted in a graph.
- 14:21, 8 June 2010 diff hist +53 N File:iRefIndex-0.83-path-selector.png The path selector for search results producing paths. current
- 12:37, 8 June 2010 diff hist +1,422 iRefScape 0.8 Further edits, tidying.
- 11:37, 8 June 2010 diff hist +2,254 iRefScape 0.8 Various formatting and other changes/updates.
- 11:13, 8 June 2010 diff hist 0 File:iRefIndex-0.83-node-attributes-close-up-closed.png uploaded a new version of "File:iRefIndex-0.83-node-attributes-close-up-closed.png": The location of the node attributes menu. current
- 10:58, 8 June 2010 diff hist +30 N File:iRefIndex-0.83-node-attributes-close-up-open.png The open node attributes menu. current
- 10:57, 8 June 2010 diff hist +41 N File:iRefIndex-0.83-node-attributes-close-up-closed.png The location of the node attributes menu.
- 09:50, 2 June 2010 diff hist +8 m Plugin test cases 0.8 Fixed syntax to make query inputs clearer.
- 12:40, 21 May 2010 diff hist +1,219 Bioscape Issues and Tasks Added a task list.
- 12:26, 21 May 2010 diff hist +276 N iRefIndex Issues and Notes New page: This document describes ongoing work to improve the iRefIndex software. == Tasks == * Validation documentation * Fix/improve SaxValidator to automate troubleshooting * Write a top-level ...
- 12:24, 21 May 2010 diff hist +99 iRefIndex Development Added link to a new page.
- 17:19, 18 May 2010 diff hist +2 m README iRefIndex Feedback 7.0 Fixed syntax. current
- 17:17, 18 May 2010 diff hist +2 m README iRefIndex MITAB experiment proposal for 7.0 →Changes from last version: Formatting changes.
- 17:16, 18 May 2010 diff hist +2 m README iRefIndex MITAB 7.0 →Changes from last version: Formatting changes. current
- 17:15, 18 May 2010 diff hist +51 Statistics iRefIndex 7.0 →Summary: Changed last updated date.
- 15:34, 14 May 2010 diff hist +595 Bioscape Configuration →Bioscape: Updated the configuration script instructions.
- 13:03, 28 April 2010 diff hist +1,663 iRefIndex Maintenance Added some recommendations.
- 17:18, 27 April 2010 diff hist +235 iRefIndex Maintenance Restructured somewhat, added remark about non-existent alternatives.
- 17:14, 26 April 2010 diff hist +419 iRefIndex Maintenance Added XtraBackup notes.
- 14:21, 26 April 2010 diff hist +359 iRefIndex Maintenance →Moving Tables into Separate Table Files: Added conclusion about the table optimisation approach.
- 13:36, 26 April 2010 diff hist +416 iRefIndex Maintenance →Moving Tables into Separate Table Files: Added notes about the outcome of table optimisation.
- 11:58, 23 April 2010 diff hist +1,255 iRefIndex Maintenance Added table moving notes.
- 14:24, 21 April 2010 diff hist +232 Bioscape Configuration →Web Interface: Moved preparation script, added system package notes.
- 12:20, 21 April 2010 diff hist +3,768 N Bioscape Configuration Moved from the installation page, removing the database configuration section (now redundant).
- 12:19, 21 April 2010 diff hist -3,889 Bioscape Installation Moved configuration information to another page.
- 12:19, 21 April 2010 diff hist +29 Bioscape Manual Added new page.
- 10:51, 20 April 2010 diff hist +296 iRefIndex Maintenance →Dumping and Restoring Databases: Added background-capable commands.
- 10:06, 20 April 2010 diff hist +843 iRefIndex Maintenance Added dump/restore recommendations.
- 16:51, 16 April 2010 diff hist -3 Bioscape Installation →Quick Start: Fixed command options.
- 16:44, 16 April 2010 diff hist +804 Bioscape Installation →PostgreSQL: Added notes about encoding/locale issues and cluster reinitialisation.
- 13:24, 29 March 2010 diff hist +4,774 N Sources iRefIndex 7.0 Initial version for 7.0.
- 13:19, 29 March 2010 diff hist +64 Sources and Issues Next Release Added variable usage for the last edited date.
- 17:47, 26 March 2010 diff hist +751 Bioscape Result Assessment →Comparing BioCreative Results and Bioscape Results: Added ambiguity result set notes.
- 19:07, 23 March 2010 diff hist +2,512 iRefIndex MITAB2.5 Parser Added schema description.
- 18:35, 23 March 2010 diff hist +11 iRefIndex MITAB2.5 Parser →Creating the Database: Using preferred option to create the database.
- 18:24, 23 March 2010 diff hist +9 README iRefIndex MITAB 7.0 →Column number: 1 (uidA): ROGID of complex is RIGID.
- 18:20, 23 March 2010 diff hist +19 README iRefIndex MITAB 7.0 →Column number: 1 (uidA): Changed the wording slightly, reformatted.
- 17:05, 23 March 2010 diff hist +114 README iRefIndex MITAB 7.0 →Column number: 14 (interactionIdentifiers): Changed example to include an iRefIndex identifier.
- 15:03, 23 March 2010 diff hist -67 README iRefIndex MITAB 7.0 →Column number: 14 (interactionIdentifiers): Changed FOUND to - for unavailable identifiers.
- 12:01, 23 March 2010 diff hist +28,869 N README iRefIndex MITAB 7.0 Initial version for 7.0.
- 16:54, 19 March 2010 diff hist +78 README iRefIndex MITAB 6.1 →Understanding the iRefIndex MITAB format: Added full text link.
- 17:24, 18 March 2010 diff hist +82 iRefIndex Maintenance Added another solution link.
- 14:47, 18 March 2010 diff hist +449 README iRefIndex MITAB 6.1 →Understanding the iRefIndex MITAB format: Added column summary table.
- 14:48, 16 March 2010 diff hist +144 iRefIndex Output and Statistics →Running PSI_MI_TAB_Maker: Added note about table preparation.
- 14:11, 15 March 2010 diff hist +41 Bioscape Result Assessment →Isolating Correct and Incorrect Bioscape Results: Added true positive distinctions.
- 19:17, 10 March 2010 diff hist +3,089 Bioscape Result Assessment Added BioCreative import details.
- 14:14, 10 March 2010 diff hist +95 iRefIndex Output and Statistics →Running BioPSI_Suplimenter to Produce Statistics: Added note about this step being optional for a completed build process.
- 16:32, 9 March 2010 diff hist +374 iRefIndex Build Process →ROG_ass + RIG_fill+ make Cy: Added note about propagating data from the full version when building the free version.
- 16:24, 9 March 2010 diff hist +207 iRefIndex Build Process →Running BioPSI_Suplimenter (continued): Added workaround.
- 15:54, 9 March 2010 diff hist +13,474 N Statistics iRefIndex free 7.0 Tentative statistics export.
- 11:56, 9 March 2010 diff hist -341 iRefIndex Build Process →ROG_ass + RIG_fill+ make Cy: Simplified Eutils advice.
- 14:57, 1 March 2010 diff hist +70 iRefIndex Build Process →BioGrid: Used a generic filename.
- 11:47, 1 March 2010 diff hist -9 iRefIndex Build Process →BioGrid: Changed ORGANISM to ALL.
- 18:48, 25 February 2010 diff hist +1,016 Bioscape Methods Added filtering and scoring notes.
- 14:01, 25 February 2010 diff hist +1,449 iRefIndex Build Process Added post-parsing validation measures, notes about free/excluded data sources. Removed CORUM preprocessing note.
- 12:44, 25 February 2010 diff hist +53 iRefIndex Build Process →Manual loading of data: Tidied formatting.
- 14:31, 22 February 2010 diff hist +273 iRefIndex Build Process →Running SaxValidator: Added notes about invalid files.
- 19:42, 18 February 2010 diff hist -688 iRefIndex Build Process →Running StaxPSIXML: The CORUM-specific fix does not seem to be necessary on the recently downloaded file.
- 18:11, 18 February 2010 diff hist 0 m iRefIndex Build Process Changed dates and date formats.
- 14:17, 18 February 2010 diff hist +427 iRefIndex Build Process →Fill Bind info: Added notes about the "Base loc" and "Date info" fields.
- 14:03, 18 February 2010 diff hist +579 iRefIndex Build Process →Manual Downloads: Added notes about BIND Translation.
- 16:40, 17 February 2010 diff hist +802 iRefIndex Build Process Added build instructions. Made separate build/running sections.
- 16:22, 17 February 2010 diff hist +1 iRefIndex Build Process →Validation and integrity checks: Changed formatting and date format.
- 14:04, 17 February 2010 diff hist +288 Text Mining Resources Added NLTK-related resources, Wikipedia pronoun page link. current
- 13:59, 17 February 2010 diff hist +1,480 N iRefIndex Maintenance Added a page about maintenance issues.
- 13:41, 17 February 2010 diff hist +28 iRefIndex Manual Added link to a new page.
- 16:55, 16 February 2010 diff hist 0 iRefIndex Release Process Moved feedback section.
- 15:29, 16 February 2010 diff hist -5 iRefIndex Build Process →Building SHA: Changed output directory.
- 16:22, 12 February 2010 diff hist +896 Bioscape Tokenisation →Adopting "Lossy" Tokenisation: Added notes on suitable filtering of tokens.
- 15:30, 12 February 2010 diff hist +1,461 Bioscape Tokenisation Added more details of the different potential tokenisation approaches.
- 18:51, 11 February 2010 diff hist +16 Sources and Issues Next Release →Interaction related resources: Fixed/added dates.
- 14:51, 11 February 2010 diff hist +25 Sources and Issues Next Release →Interaction related resources: Updated versions and dates.
- 14:14, 11 February 2010 diff hist +118 Sources and Issues Next Release →Sequence related resources: Updated versions and dates.
- 14:39, 10 February 2010 diff hist +468 Bioscape Searching →Selecting Search Resources: Added a note about stop word-based terms.
- 18:23, 9 February 2010 diff hist +68 iRefIndex Build Process →Downloading the Source Data: Adjustments to the source lists.
- 12:33, 9 February 2010 diff hist +3 iRefIndex Build Process →DIP: Fixed filename.
- 18:49, 8 February 2010 diff hist 0 iRefIndex Build Process →MIPS: Fixed pathname in example.
- 17:30, 8 February 2010 diff hist +52 iRefIndex Build Process →OPHID: Added deprecation note.
- 17:29, 8 February 2010 diff hist -97 iRefIndex Build Process →I2D: Fixed commands for specific filename details.
- 17:11, 8 February 2010 diff hist +674 iRefIndex Build Process →Manual Downloads: Added I2D section.
- 15:21, 8 February 2010 diff hist +124 Text Mining Resources
- 12:29, 4 February 2010 diff hist +115 Text Mining Resources
- 19:27, 29 January 2010 diff hist +234 Text Mining Resources
- 19:24, 29 January 2010 diff hist +368 Text Mining Resources
- 16:56, 26 January 2010 diff hist +1,232 N Displaying Bioscape Search Results Initial notes.
- 16:45, 26 January 2010 diff hist +42 Bioscape Manual Added link to a new page.
- 13:15, 26 January 2010 diff hist -260 iRefIndex Build Process Updated the instructions, removed FTPtransfer modification step, added data directory argument.
- 10:51, 26 January 2010 diff hist -14 m README iRefIndex expanded MITAB proposal →Understanding the iRefIndex MITAB format: Fixed formatting, or at least prevented weird list construction.
- 18:23, 21 January 2010 diff hist +827 Bioscape Web Resources Added templates.
- 16:15, 21 January 2010 diff hist +674 iRefScape 0.6 Added font rendering tip, distribution package details.
- 13:53, 21 January 2010 diff hist +290 Text Mining Resources →Text Search Resources: Added PMC open access resource information.
- 13:47, 21 January 2010 diff hist +133 Text Mining Resources →Text Search Resources: Added BioMed Central information.
- 16:20, 20 January 2010 diff hist +28 iRefScape 0.6 →Windows Vista and Windows XP: Minor formatting changes.
- 14:50, 20 January 2010 diff hist +114 iRefScape 0.6 →Usage: Added dialogues. Reordered sections, introducing advanced mode first.
- 13:47, 20 January 2010 diff hist 0 File:IRefIndex-Cytoscape-Advanced.png uploaded a new version of "Image:IRefIndex-Cytoscape-Advanced.png": The iRefIndex plugin panel in advanced mode. current
- 13:46, 20 January 2010 diff hist +44 N File:IRefIndex-Cytoscape-Advanced.png The iRefIndex plugin panel in advanced mode.
- 13:41, 20 January 2010 diff hist +216 iRefScape 0.6 →Usage: Moved images around, edited the wording.
- 13:18, 20 January 2010 diff hist +355 iRefScape 0.6 →Usage: Added dialogues.
- 12:59, 20 January 2010 diff hist +38 N File:IRefIndex-Cytoscape-Wizard-step5.png Step 5 of the iRefIndex plugin wizard. current
- 12:59, 20 January 2010 diff hist +38 N File:IRefIndex-Cytoscape-Wizard-step4.png Step 4 of the iRefIndex plugin wizard. current
- 12:58, 20 January 2010 diff hist +38 N File:IRefIndex-Cytoscape-Wizard-step3.png Step 3 of the iRefIndex plugin wizard. current
- 12:57, 20 January 2010 diff hist +38 N File:IRefIndex-Cytoscape-Wizard-step2.png Step 2 of the iRefIndex plugin wizard. current
- 12:55, 20 January 2010 diff hist +37 N File:IRefIndex-Cytoscape-Wizard.png The iRefIndex plugin wizard dialogue. current
- 12:53, 20 January 2010 diff hist +57 iRefScape 0.6 Added breaks in the formatting. Moved some images around. Minor edits.
- 12:43, 20 January 2010 diff hist +265 iRefScape 0.6 →Completing the installation: Added dialogues.
- 12:42, 20 January 2010 diff hist 0 File:IRefIndex-Cytoscape-Success.png uploaded a new version of "Image:IRefIndex-Cytoscape-Success.png": A successful iRefIndex plugin installation. current
- 12:39, 20 January 2010 diff hist +50 N File:IRefIndex-Cytoscape-Success.png A successful installation of the iRefIndex plugin.
- 12:36, 20 January 2010 diff hist +39 N File:IRefIndex-Cytoscape-Download.png The iRefIndex plugin download dialogue. current
- 12:35, 20 January 2010 diff hist +44 N File:IRefIndex-Cytoscape-Location.png The iRefIndex plugin data location dialogue. current
- 12:32, 20 January 2010 diff hist +249 iRefScape 0.6 →Using Cytoscape plugin manager: Added dialogues.
- 12:28, 20 January 2010 diff hist +40 N File:IRefIndex-Cytoscape-Bookmark-manager.png The Cytoscape Bookmark manager dialogue. current
- 12:28, 20 January 2010 diff hist +45 N File:IRefIndex-Cytoscape-Plugin-Download-Sites.png The Cytoscape Plugin Download Sites dialogue. current
- 12:27, 20 January 2010 diff hist +38 N File:IRefIndex-Cytoscape-Manage-Plugins.png The Cytoscape Manage Plugins dialogue. current
- 12:23, 20 January 2010 diff hist +312 iRefScape 0.6 →Using Cytoscape plugin manager: Added uninstall notes.
- 12:24, 19 January 2010 diff hist +279 Text Mining Resources
- 16:31, 18 January 2010 diff hist +164 Text Mining Resources
- 19:48, 18 December 2009 diff hist +1,259 Bioscape Tokenisation Added gene keyword-related note.
- 18:05, 16 December 2009 diff hist +867 Bioscape Scoring Techniques →Assuming the Presence of Gene Symbols: Added gene summary-related example.
- 17:58, 16 December 2009 diff hist +1,039 Bioscape Scoring Techniques →Acronym Mentions and Techniques: Added awkward acronym detection case.
- 17:43, 16 December 2009 diff hist +935 Bioscape Scoring Techniques Added example involving gene symbol assertions.
- 15:26, 15 December 2009 diff hist +43 Bioscape Scoring Techniques →Acronym Mentions and Techniques: Moved example and tagged it with a method.
- 15:31, 14 December 2009 diff hist +1,275 Bioscape Scoring Techniques Added disqualifier-related techniques.
- 14:20, 14 December 2009 diff hist +1,129 Bioscape Scoring Techniques Added an example of parentheses-related scoring.
- 14:05, 14 December 2009 diff hist +1,123 Bioscape Searching Techniques →Bioentity Inference: Added another example.
- 13:56, 14 December 2009 diff hist +94 Bioscape Scoring Techniques →PubMed #7512734: Updated the example given newer results.
- 13:51, 14 December 2009 diff hist +2,550 Bioscape Searching Techniques Added more examples.
- 13:33, 14 December 2009 diff hist +689 Bioscape Searching Techniques Added bioentity-specific example.
- 17:20, 9 December 2009 diff hist +474 N Bioinformatics Data Resources New page: * [http://jura.wi.mit.edu/entrez_gene/entrezgene.html Entrez Gene Database Description and Files] - scripts and a schema for parsing Entrez Gene data and populating a database * [http://en... current
- 16:13, 9 December 2009 diff hist +36 Bioscape Manual Added new document.
- 16:13, 9 December 2009 diff hist +1,198 N DiG: Disease groups/Bioscape Notes New page: Some notes related to disease groups and Bioscape. ---- Possible MeSH terms: * Fanconi Anemia Search for FANCD2 and "Fanconi Anemia": * [http://bioscape.uio.no/cgi-bin/bsweb.cgi/quali...
- 17:50, 7 December 2009 diff hist +436 Bioscape Tokenisation Added example issue.
- 19:31, 4 December 2009 diff hist +2,370 Bioscape Searching Techniques Added possible synonym definition technique.
- 18:36, 4 December 2009 diff hist +1,697 Bioscape Scoring Techniques →Acronym Mentions and Techniques: Added disambiguation techniques.
- 16:05, 4 December 2009 diff hist +11 m Bioscape Searching Techniques →PubMed #10484778: Fixed quoted text in table.
- 17:59, 3 December 2009 diff hist +1,470 Bioscape Searching Techniques Added more examples.
- 17:41, 3 December 2009 diff hist +37 Bioscape Manual Added link to new page.
- 17:41, 3 December 2009 diff hist +3,359 N Bioscape Searching Techniques New page: A number of searching techniques are applied to find textual mentions of entities or concepts, particularly those where the nature of the searching is speculative, meaning that no predefin...
- 15:07, 3 December 2009 diff hist 0 m Bioscape Manual Moved development link.
- 15:18, 2 December 2009 diff hist +136 Bioscape Development →Adding New Search Result Types: Added Web translations note.
- 15:05, 2 December 2009 diff hist +176 Bioscape Development →Adding New Search Result Types: Added database template note.
- 09:00, 2 December 2009 diff hist +101 Bioscape Scoring Techniques Added missing suggestions.
- 16:33, 1 December 2009 diff hist +3,374 Bioscape Scoring Techniques Added more examples.
- 13:28, 26 November 2009 diff hist +3,794 Bioscape Scoring Techniques Added some acronym mention techniques.
- 15:42, 24 November 2009 diff hist +762 Bioscape Scoring Techniques Added chromosome information correspondence.
- 16:41, 23 November 2009 diff hist +1,664 Bioscape Scoring Techniques Added Gene Ontology-related techniques.
- 13:29, 23 November 2009 diff hist +2,974 Bioscape Scoring Techniques Added more examples.
- 12:55, 23 November 2009 diff hist -127 Bioscape Methods Replaced section, linking to a more comprehensive document.
- 12:54, 23 November 2009 diff hist +2,093 N Bioscape Scoring Techniques Started a collection of scoring techniques.
- 12:31, 23 November 2009 diff hist +94 Bioscape Manual Added missing links plus new document.
- 12:29, 23 November 2009 diff hist +42 Bioscape Workflow Added links to methods/scoring documentation.
- 17:07, 17 November 2009 diff hist +1,435 N Bioscape Result Assessment New page: The suggestions produced by Bioscape's search activities can be assessed subject to the availability of "gold standard" data which confirms whether each particular result can be regarded a...
- 13:24, 17 November 2009 diff hist +33 Bioscape Manual Added link to new page.
- 18:29, 16 November 2009 diff hist 0 File:Bioscape-advanced-search-dialogue.png uploaded a new version of "Image:Bioscape-advanced-search-dialogue.png": The Bioscape advanced search dialogue. current
- 18:26, 16 November 2009 diff hist +440 Using the Bioscape Web Application →Gene Summaries: Added ad-hoc details. current
- 18:25, 16 November 2009 diff hist +46 N File:Bioscape-gene-summary-adhoc-detail.png Qualifier details for a Bioscape gene summary. current
- 18:21, 16 November 2009 diff hist +75 N File:Bioscape-gene-summary-adhoc.png The Bioscape gene summary with a qualifier term used to filter the results. current
- 18:16, 16 November 2009 diff hist 0 File:Bioscape-gene-summary.png uploaded a new version of "Image:Bioscape-gene-summary.png": The Bioscape gene summary. current
- 18:16, 16 November 2009 diff hist 0 File:Bioscape-search-disambiguation-dialogue.png uploaded a new version of "Image:Bioscape-search-disambiguation-dialogue.png": The Bioscape search disambiguation dialogue. current
- 18:14, 16 November 2009 diff hist +1,409 Using the Bioscape Web Application →Searching: Updated search dialogue, added ad-hoc field description.
- 17:54, 16 November 2009 diff hist +59 N File:Bioscape-search-dialogue-adhoc.png The Bioscape search dialogue with ad-hoc search facilities. current
- 20:29, 13 November 2009 diff hist +3,142 Bioscape Workflow Added labelling and data hierarchy notes.
- 20:07, 13 November 2009 diff hist +410 N Supported Data Sources Incomplete draft.
- 19:45, 13 November 2009 diff hist +129 Bioscape Data Sources Added link to new page.
- 19:18, 11 November 2009 diff hist +659 Bioscape Tokenisation
- 15:03, 11 November 2009 diff hist +1,423 N Bioscape Tokenisation Initial notes.
- 14:52, 11 November 2009 diff hist +163 Bioscape Searching →Tokenisation: Added link to new page.
- 14:48, 11 November 2009 diff hist +61 Bioscape Indexing Qualified the B-tree remarks.
- 17:47, 6 November 2009 diff hist +716 Bioscape Searching →Phrases and Validation: Added validation example.
- 13:03, 6 November 2009 diff hist +1,612 Bioscape Data Sources Added export and extraction notes, overview.
- 12:51, 6 November 2009 diff hist +908 Bioscape Searching Added reading and writing notes.
- 15:39, 5 November 2009 diff hist +1,496 Bioscape Searching →Locating Matches: Added the start of the description of phrases and validation.
- 15:04, 5 November 2009 diff hist +552 Bioscape Searching Modified locator tasks.
- 14:57, 5 November 2009 diff hist +2,126 Bioscape Searching Added derived term generation description, variation generation summary. Reordered sections.
- 14:04, 5 November 2009 diff hist +1,271 Bioscape Searching Added overview/workflow diagrams.
- 19:20, 4 November 2009 diff hist +1,812 Bioscape Searching →Variations within Search Terms: Added a description of the variation mechanisms.
- 17:36, 4 November 2009 diff hist +609 Bioscape Searching →Search Overview: Added speculative search diagram and description.
- 14:04, 3 November 2009 diff hist +1,065 Bioscape Searching Added overview/workflow.
- 13:23, 30 October 2009 diff hist +1 Bioscape Indexing Updated Lucene format link, fixed wording.
- 12:59, 30 October 2009 diff hist +493 Bioscape Indexing Added indexing solution file format references.
- 13:20, 29 October 2009 diff hist +1,746 Bioscape Indexing Added identifier conversion notes.
- 13:45, 27 October 2009 diff hist +98 Text Indexing Resources Added Tokyo Dystopia. current
- 13:43, 26 October 2009 diff hist +10,581 iRefIndex/PBR Notes Added explanatory queries, details. Moved observations to the top. current
- 11:00, 26 October 2009 diff hist +22 iRefIndex/PBR Notes →Observations: Fixed first observation: "BIND identifiers" -> "distinct human interaction identifiers".
- 17:35, 23 October 2009 diff hist -72 MediaWiki:CustomEditTemplates The CustomEdit extension seems too restrictive for our purposes. current
- 15:49, 23 October 2009 diff hist +2,805 N Bioscape Data Types New page: Bioscape is aware of a number of different data types, focusing mostly on the notion of a bioentity, but handling that and other kinds of data. These data types are defined in the <tt>bios...
- 15:27, 23 October 2009 diff hist +26 Bioscape Manual Added link to a new page.
- 13:00, 23 October 2009 diff hist +98 Nm UNTITLED Dummy article created for Simple Forms extension current
- 12:29, 23 October 2009 diff hist +72 N MediaWiki:CustomEditTemplates New page: * Template:BioinformaticsPerson - used to edit bioinformatics people
- 16:34, 22 October 2009 diff hist +2,454 iRefIndex/PBR Notes →Retrieving BIND Identifiers: Added query for identifiers without considering interactions.
- 17:59, 21 October 2009 diff hist +596 Bioscape Searching Added section.
- 13:07, 21 October 2009 diff hist +407 Bioscape Indexing →Efficient access to index storage: Added a note about the retrieval of complete result sets.
- 12:14, 21 October 2009 diff hist +2,119 Bioscape Indexing →Convenient access to document identifiers: Added an example of the genuine identifier retrieval problem.
- 17:37, 20 October 2009 diff hist +260 m Bioscape Methods Changed formatting of tables.
- 17:33, 20 October 2009 diff hist -16 m Bioscape Web Resources Changed formatting of tables.
- 17:32, 20 October 2009 diff hist -539 m Bioscape Methods Changed formatting of tables.
- 17:30, 20 October 2009 diff hist +16 m Bioscape Web Resources Changed formatting of tables.
- 17:28, 20 October 2009 diff hist +760 m Bioscape Methods Formatting changes to tables.
- 17:28, 19 October 2009 diff hist +242 Text Indexing Resources Added link, category.
- 17:13, 19 October 2009 diff hist +112 Bioscape Manual Made a separate topics list for development, adding links to various new and related pages.
- 17:12, 19 October 2009 diff hist +149 Text Mining Resources Added link to summary. Added category.
- 17:10, 19 October 2009 diff hist +181 Bioscape Indexing Added link to new page.
- 17:06, 19 October 2009 diff hist +1,011 Text Indexing Resources
- 15:52, 19 October 2009 diff hist +2,176 N Text Indexing Resources New page: A considerable number of text indexing solutions exist. This document discusses some of the more widely-known open source solutions. * [http://www.htdig.org/ ht://Dig] - ''a search engine...
- 11:57, 19 October 2009 diff hist +564 Bioscape Searching →Locating Matches: Added a brief description of locators, sources and phrases.
- 12:04, 16 October 2009 diff hist +2,025 N Bioscape Web Resources A description of the bsweb package organisation.
- 11:44, 16 October 2009 diff hist +29 Bioscape Manual Added new document.
- 16:03, 15 October 2009 diff hist +786 Text Mining Resources →Text Search Resources: Added MEDIE.
- 15:37, 15 October 2009 diff hist +1,627 Text Mining Resources →Notes from the Text Mining Tutorial at EBI: Added more resources with separate lists for different resource types.
- 12:51, 15 October 2009 diff hist +3,319 Text Mining Resources Initial notes.
- 10:50, 9 October 2009 diff hist +276 Text Mining Resources Added FreeLing and NLTK.
- 12:55, 2 October 2009 diff hist +1,616 iRefIndex/PBR Notes →Retrieving BIND Identifiers: Added queries for interaction identifiers, clarifying what the existing queries actually retrieve.
- 11:51, 2 October 2009 diff hist +28 Bioscape Manual Added link to data sources page.
- 11:50, 2 October 2009 diff hist +26 Bioscape Distribution →Data Sources: Added link.
- 11:49, 2 October 2009 diff hist +23 m Bioscape Workflow Added category.
- 11:48, 2 October 2009 diff hist +1,845 N Bioscape Workflow Added workflow information.
- 11:16, 2 October 2009 diff hist +24 Bioscape Manual Added link to new page.
- 17:20, 1 October 2009 diff hist +4,835 N Bioscape Data Sources Initial version of data sources documentation.
- 16:21, 29 September 2009 diff hist +102 Bioscape Development →Adding New Data Sources and Types: Added link to new document.
- 11:44, 28 September 2009 diff hist +86 m iRefIndex/PBR Notes →Results: Added table borders.
- 11:43, 28 September 2009 diff hist +43 m iRefIndex/PBR Notes →Observations: Added table border.
- 18:52, 25 September 2009 diff hist +105 iRefIndex/PBR Notes →Observations: Added bug link.
- 18:46, 25 September 2009 diff hist +20 iRefIndex/PBR Notes →Observations: Clarified identifier 100771 occurrence.
- 18:38, 25 September 2009 diff hist +78 iRefIndex/PBR Notes →Observations: Formatting edits.
- 16:26, 25 September 2009 diff hist +6,480 iRefIndex/PBR Notes →Queries: Added BIND identifier extraction.
- 15:19, 25 September 2009 diff hist +1,503 N Text Mining Resources New page: Some notes on open source text mining resources: * "The Text Mining Tool Evaluation project will describe the process of text mining, identify non-proprietary software that can search blo...
- 15:37, 24 September 2009 diff hist +223 iRefIndex Output and Statistics →Building PSI_MI_TAB_Maker: Added SHA dependency, library version note.
- 11:45, 23 September 2009 diff hist +465 Bioscape Indexing Added filtered index notes.
- 15:47, 22 September 2009 diff hist +22 m Bioscape Searching →Text Indexing: Added link.
- 15:46, 22 September 2009 diff hist +971 N Bioscape Indexing Initial notes.
- 14:43, 22 September 2009 diff hist +23 m Bioscape Dependencies Added category.
- 14:43, 22 September 2009 diff hist +1 m Bioscape Methods →Processing, Methods and Scoring: Tidying.
- 14:42, 22 September 2009 diff hist +23 Bioscape Status 2009 current
- 11:56, 22 September 2009 diff hist +578 N Bioscape Status 2009 New page: Some notes about the status of Bioscape in September 2009. == Changes Since 2008 == * Reorganised the code base and database schema to better support a wider range of data types in a con...
- 16:21, 21 September 2009 diff hist 0 Bioscape Methods →Result Scoring Techniques: Moved heading.
- 16:20, 21 September 2009 diff hist +1,332 Bioscape Methods →Result Scoring: Added currently used methods.
- 16:12, 21 September 2009 diff hist +932 Bioscape Methods →Sentence Scoring: Added a brief description.
- 16:05, 21 September 2009 diff hist +962 Bioscape Methods →Search Scoring: Added brief description.
- 15:55, 21 September 2009 diff hist +225 Bioscape Methods →Term Scoring: Added filtering note.
- 15:47, 21 September 2009 diff hist +1,087 Bioscape Methods →Term Scoring: Added currently used methods.
- 14:30, 21 September 2009 diff hist +1,788 iRefIndex/PBR Notes Restricted interactors to 9606 for the "human" BIND PSI-XML data.
- 13:51, 21 September 2009 diff hist +1 iRefIndex/PBR Notes →Results: Restricted to 9606 interactors.
- 13:48, 21 September 2009 diff hist -7 iRefIndex/PBR Notes →Queries: Fixed query.
- 13:41, 21 September 2009 diff hist +1,706 iRefIndex/PBR Notes →Queries: Restrict to 9606 interactors.
- 12:18, 21 September 2009 diff hist +1,435 iRefIndex/PBR Notes Added interactors.
- 11:02, 21 September 2009 diff hist +774 iRefIndex/PBR Notes
- 10:34, 21 September 2009 diff hist +889 N iRefIndex/PBR Notes New page: Importing MITAB output from the iRefIndex 5.1 build and a build done using the BIND PSI-XML data, then comparing the interaction details for BIND, the following distribution is observed: ...
- 11:38, 15 September 2009 diff hist +4 m iRefIndex Release Process →Testing the Output: Fixed formatting.
- 17:02, 14 September 2009 diff hist +385 iRefIndex/PBR Next attempt. current
- 16:01, 10 September 2009 diff hist +7,710 N iRefIndex/PBR New page: == Interactions == {| | BIND||9645 |- | BIOGRID||0 || 0 |- | DIP||0 || 0 || 0 |- | HPRD||0 || 0 || 0 || 0 |- | INTACT||0 || 0 || 0 || 0 || 0 |- | MINT||0 || 0 || 0 || 0 || 0...
- 15:59, 9 September 2009 diff hist +181 iRefIndex Build Process →Running StaxPSIXML: Added link to the development documentation.
- 15:20, 9 September 2009 diff hist +352 iRefIndex Build Process →Building StaxPSIXML: Added library version notes.
- 16:05, 4 September 2009 diff hist +364 iRefIndex Build Process →Building BioPSI_Suplimenter: Added MySQL Connector/J version notes.
- 15:51, 4 September 2009 diff hist -5 iRefIndex Build Process →Building BioPSI_Suplimenter: The SHA build file seems to use the dist directory now.
- 15:35, 20 August 2009 diff hist +628 Bioscape Searching →Variations within Search Terms: Added initial example, some description.
- 14:50, 20 August 2009 diff hist +950 Bioscape Searching →Matching Strategies: Added examples.
- 14:15, 20 August 2009 diff hist +46 Bioscape Searching →Tokenisation: Added space around table and changed the preceding text.
- 15:50, 13 August 2009 diff hist +1,382 Bioscape Searching →Speculative Searching: Added a description.
- 15:02, 13 August 2009 diff hist +875 Bioscape Searching →Predefined Searching Using Lexicons: Added querying notes.
- 13:13, 13 August 2009 diff hist +2,382 Bioscape Searching Added matching strategies and indexing details.