User contributions
From irefindex
- 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.
- 18:19, 25 July 2009 diff hist +427 Bioscape Searching →Tokenisation: Edit table.
- 18:09, 24 July 2009 diff hist +5,009 N Bioscape Searching Initial version of searching documentation.
- 17:07, 24 July 2009 diff hist +25 Bioscape Manual Added searching document.
- 17:07, 24 July 2009 diff hist +23 Using the Bioscape Web Application Added category.
- 17:06, 24 July 2009 diff hist 0 Using the Bioscape Web Application Moved images.
- 17:04, 24 July 2009 diff hist +48 Using the Bioscape Web Application →Searching: Link to section.
- 17:02, 24 July 2009 diff hist +854 Using the Bioscape Web Application Added advanced search details.
- 16:54, 24 July 2009 diff hist +38 N File:Bioscape-advanced-search-dialogue.png The Bioscape advanced search dialogue.
- 16:17, 24 July 2009 diff hist +558 Using the Bioscape Web Application Added more images.
- 16:16, 24 July 2009 diff hist +36 N File:Bioscape-method-scores-for-result.png Method scores for a specific result. current
- 16:10, 24 July 2009 diff hist +38 N File:Bioscape-document-versions.png Showing document versions in Bioscape. current
- 16:08, 24 July 2009 diff hist +53 N File:Bioscape-evidence-document.png An interaction evidence document summary in Bioscape. current
- 16:08, 24 July 2009 diff hist +46 N File:Bioscape-scored-document.png A scored results document summary in Bioscape. current
- 16:07, 24 July 2009 diff hist +38 N File:Bioscape-search-document.png A search document summary in Bioscape. current
- 16:07, 24 July 2009 diff hist +31 N File:Bioscape-index-document-2.png A document summary in Bioscape. current
- 15:53, 24 July 2009 diff hist +38 N File:Bioscape-index-document.png An index document summary in Bioscape. current
- 15:48, 24 July 2009 diff hist +132 Using the Bioscape Web Application Added layout elements to stop images from trespassing on other sections.
- 15:44, 24 July 2009 diff hist +83 Using the Bioscape Web Application →Mention Sentences: Added image.
- 15:43, 24 July 2009 diff hist +32 N File:Bioscape-mention-sentences.png Bioscape mention sentences view. current
- 15:01, 24 July 2009 diff hist +64 Using the Bioscape Web Application →Gene Summaries: Added image.
- 15:01, 24 July 2009 diff hist +24 N File:Bioscape-gene-summary.png A Bioscape gene summary.
- 14:58, 24 July 2009 diff hist +111 Using the Bioscape Web Application →Search Disambiguation: Added image.
- 14:57, 24 July 2009 diff hist +81 Using the Bioscape Web Application →Searching: Added image.
- 14:56, 24 July 2009 diff hist +44 N File:Bioscape-search-disambiguation-dialogue.png The Bioscape search disambiguation dialogue.
- 14:54, 24 July 2009 diff hist +29 N File:Bioscape-search-dialogue.png The Bioscape search dialogue. current
- 14:49, 24 July 2009 diff hist +4,007 Using the Bioscape Web Application Added more feature descriptions.
- 12:35, 24 July 2009 diff hist +3,411 Using the Bioscape Web Application Added more information about various features.
- 11:36, 24 July 2009 diff hist +1,170 N Using the Bioscape Web Application Initial version of the help for the Web application.
- 11:25, 24 July 2009 diff hist +41 Bioscape Manual
- 11:24, 24 July 2009 diff hist -76 Donaldson Group
- 11:22, 24 July 2009 diff hist -478 BioScape Redirect to Bioscape. current
- 11:21, 24 July 2009 diff hist +382 Bioscape Moved Web application details to this page.
- 15:54, 23 July 2009 diff hist +55 Bioscape Development →Adding New Search Result Types: Add policy class note.
- 12:40, 22 July 2009 diff hist +1,722 Bioscape Methods Added descriptive text for result scoring.
- 12:37, 22 July 2009 diff hist +2,356 Bioscape Methods →Term Scoring: Added some descriptive text.
- 12:36, 22 July 2009 diff hist +86 Bioscape Methods →Processing, Methods and Scoring: Renamed "name" to "term".
- 17:50, 21 July 2009 diff hist -1,800 Bioscape Development Revised version details.
- 17:33, 21 July 2009 diff hist -134 Bioscape Development →Adding New Data Sources and Types: Revised version information.
- 17:27, 21 July 2009 diff hist -968 Bioscape Development →Adding New Search Result Types: Revised version details.
- 17:14, 21 July 2009 diff hist -1 Bioscape Development →Adding New Scoring Methods: Updated for revised distribution layout.
- 17:04, 21 July 2009 diff hist -2,966 Bioscape Distribution Revised distribution details.
- 16:47, 21 July 2009 diff hist +28 Bioscape Manual Added dependencies.
- 16:46, 21 July 2009 diff hist +1,774 N Bioscape Dependencies Revised version dependencies.
- 16:44, 21 July 2009 diff hist +164 Bioscape Installation →Web Interface: Added resource preparation.
- 14:48, 21 July 2009 diff hist +624 Bioscape Installation Added Web interface configuration.
- 14:31, 21 July 2009 diff hist -4,881 Bioscape Installation New version documentation.
- 16:43, 6 July 2009 diff hist +147 BioScape Updated browser note.
- 13:44, 22 June 2009 diff hist -13 Donaldson Group Change Bioscape link.
- 08:53, 8 June 2009 diff hist +11,544 N Statistics iRefIndex 4.0 Statistics for the free release.
- 15:35, 5 June 2009 diff hist 0 N File:Tools.svg current
- 15:35, 5 June 2009 diff hist 0 N File:PD-icon.svg current
- 15:34, 5 June 2009 diff hist 0 N File:PD-Help icon.png current
- 15:34, 5 June 2009 diff hist 0 N File:M-en-userlinks.png current
- 15:34, 5 June 2009 diff hist 0 N File:M-en-sidebar.png current
- 15:34, 5 June 2009 diff hist 0 N File:M-en-recentchanges.png current
- 15:34, 5 June 2009 diff hist 0 N File:M-en-pagetabs.png current
- 15:34, 5 June 2009 diff hist 0 N File:M-en-interwiki lang.png current
- 15:33, 5 June 2009 diff hist 0 N File:Geographylogo.png current
- 15:33, 5 June 2009 diff hist 0 N File:Example-white-bg.jpg current
- 15:33, 5 June 2009 diff hist 0 N File:Example.jpg current
- 15:33, 5 June 2009 diff hist 0 N File:Bulbgraph.png current
- 15:24, 5 June 2009 diff hist +1,552 m Help:Contents Reverted edits by PaulBoddie (Talk); changed back to last version by Emufarmers current
- 15:18, 5 June 2009 diff hist 0 m Template:GFDL 1 revision current
- 15:18, 5 June 2009 diff hist 0 m Template:GPL 1 revision current
- 15:18, 5 June 2009 diff hist 0 m Category:Help/categories 1 revision current
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- 15:18, 5 June 2009 diff hist 0 m File:Example-white-bg.jpg 1 revision current
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- 15:18, 5 June 2009 diff hist 0 m Help:Tables 1 revision current
- 15:18, 5 June 2009 diff hist 0 m Help:Sysops and permissions 1 revision current
- 15:18, 5 June 2009 diff hist 0 m Help:Sysop deleting and undeleting 1 revision current
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- 15:18, 5 June 2009 diff hist 0 m Help:Starting a new page 1 revision current
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- 10:17, 4 June 2009 diff hist +85 iRefIndex Output and Statistics Added new section.
- 11:54, 28 May 2009 diff hist +57 N File:QCR2 HUMAN initial.png Initial view of the results from a search for QCR2_HUMAN. current
- 10:58, 18 May 2009 diff hist +93 N MBV3070 Added link to slides. Sorry about the proprietary format!
- 10:53, 18 May 2009 diff hist 0 N File:Lecture 1 - What Perl can do.ppt
- 08:47, 15 May 2009 diff hist +148 iRefIndex Build Process →Downloading the Source Data: Added free/proprietary source list.
- 08:39, 15 May 2009 diff hist -34 iRefIndex Build Process →Manual Downloads: Fixed sources link.
- 12:38, 12 May 2009 diff hist -1 Bioseminar Moved April seminars to the "previous" section.
- 13:10, 27 April 2009 diff hist +599 Bioseminar Update talk title. Reordered table sections. Minor edits.
- 11:20, 22 April 2009 diff hist 0 README iRefIndex MITAB 3.0 →Known Issues: Fixed formatting. current
- 16:09, 26 March 2009 diff hist +163 Bioscape Installation →Dependencies: Added NCBI tools.
- 12:17, 23 March 2009 diff hist +41 Bioseminar Added Philipp's title.
- 18:24, 12 March 2009 diff hist +907 Bioscape Methods →Result Scoring: Added notes about methods which either confirm or disambiguate mentions.
- 12:47, 10 March 2009 diff hist 0 m Donaldson Group →Local Seminar Series: Minor edits.