User contributions
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Jump to navigationJump to search- 19:01, 8 March 2010 diff hist +279 N Genes mentioned along with word in Figure or Table category New page: Right now, this seems to be the most promising approach. 'Over-association' will come from things like markers. 'Under-association' will come from lists of genes in figures or tables, bu...
- 14:28, 7 March 2010 diff hist +109 Associating genes with papers
- 16:41, 1 March 2010 diff hist +38 WormBase
- 14:36, 24 February 2010 diff hist -18 Lung Development Targets (November 2009 - February 2010) →December Targets
- 14:35, 24 February 2010 diff hist +26 Lung Development Targets (November 2009 - February 2010) →December Targets
- 14:34, 24 February 2010 diff hist +3 Lung Development Targets (November 2009 - February 2010) →December Targets
- 11:49, 24 February 2010 diff hist +30 Lung Development Targets (November 2009 - February 2010) →December Targets
- 17:20, 18 February 2010 diff hist +1 Journals
- 17:16, 18 February 2010 diff hist +27 N-Z titles
- 17:13, 18 February 2010 diff hist +15 Journals
- 16:57, 18 February 2010 diff hist +20 Journals
- 15:41, 14 February 2010 diff hist +83 Merging Papers
- 19:14, 11 February 2010 diff hist +11 Lung Development Targets (November 2009 - February 2010)
- 19:08, 11 February 2010 diff hist -1 Lung Development Targets (November 2009 - February 2010) →November Targets
- 19:06, 11 February 2010 diff hist +825 Lung Development Targets (November 2009 - February 2010) →November Targets
- 18:49, 11 February 2010 diff hist +13 Lung Development Targets (November 2009 - February 2010) →November Targets
- 18:48, 11 February 2010 diff hist +151 Lung Development Targets (November 2009 - February 2010)
- 18:42, 8 February 2010 diff hist +7 New Paper Model - Model and Changes to Pipeline
- 15:42, 8 February 2010 diff hist -4 New Paper Model - Model and Changes to Pipeline
- 14:05, 8 February 2010 diff hist +2 Journals
- 14:05, 8 February 2010 diff hist +26 Journals
- 14:04, 8 February 2010 diff hist +144 N-Z titles
- 18:08, 7 February 2010 diff hist +134 Lung Development Targets (November 2009 - February 2010)
- 17:35, 7 February 2010 diff hist +22 Lung Development Targets (November 2009 - February 2010)
- 17:33, 7 February 2010 diff hist +30 Lung Development Targets (November 2009 - February 2010)
- 17:08, 7 February 2010 diff hist +86 Lung Development Targets (November 2009 - February 2010)
- 15:14, 7 February 2010 diff hist +38 Lung Development Targets (November 2009 - February 2010)
- 00:08, 7 February 2010 diff hist +38 Ontology Annotator
- 00:08, 7 February 2010 diff hist +2 Ontology Annotator
- 00:05, 7 February 2010 diff hist +1 Ontology Annotator
- 23:52, 6 February 2010 diff hist +98 Ontology Annotator
- 23:38, 6 February 2010 diff hist +19 Gene Ontology
- 22:59, 6 February 2010 diff hist +21 Lung Development Targets (November 2009 - February 2010)
- 22:49, 6 February 2010 diff hist +38 Lung Development Targets (November 2009 - February 2010)
- 22:02, 6 February 2010 diff hist +141 Ontology Annotator →Wish List and Bug Reports, Jan-Feb 2010
- 22:00, 6 February 2010 diff hist +27 Lung Development Targets (November 2009 - February 2010)
- 21:28, 6 February 2010 diff hist +143 Lung Development Targets (November 2009 - February 2010)
- 21:11, 6 February 2010 diff hist -21 Lung Development Targets (November 2009 - February 2010)
- 21:10, 6 February 2010 diff hist +2 Lung Development Targets (November 2009 - February 2010)
- 21:08, 6 February 2010 diff hist +37 Lung Development Targets (November 2009 - February 2010)
- 19:56, 6 February 2010 diff hist +573 N Lung Development Targets (November 2009 - February 2010) New page: Lung Development Gene Annotation Progress {|border="1" cell spacing="0" cellpadding="5" align="center" !Panther ID !C. elegans Target(s) !Curator !Papers !Biological Process !Molecular Fu...
- 19:45, 6 February 2010 diff hist -339 Gene Ontology
- 19:42, 6 February 2010 diff hist +46 Gene Ontology
- 19:41, 6 February 2010 diff hist +182 Gene Ontology
- 19:56, 5 February 2010 diff hist -1 Type - mapping incoming Type
- 18:57, 5 February 2010 diff hist +102 Primary data Tag
- 18:46, 5 February 2010 diff hist +82 Type - mapping incoming Type
- 18:45, 5 February 2010 diff hist +77 Primary data Tag
- 18:43, 5 February 2010 diff hist 0 Primary data Tag
- 13:17, 5 February 2010 diff hist -1 New Paper Model - Model and Changes to Pipeline
- 18:21, 3 February 2010 diff hist +326 Journals
- 18:04, 3 February 2010 diff hist +113 Journals
- 17:55, 3 February 2010 diff hist +39 Journals
- 17:52, 3 February 2010 diff hist +161 Journals
- 17:48, 3 February 2010 diff hist +58 Journals
- 17:38, 3 February 2010 diff hist -10,348 Journals
- 17:37, 3 February 2010 diff hist +14 N-Z titles
- 17:36, 3 February 2010 diff hist +97 N-Z titles
- 17:33, 3 February 2010 diff hist +9,934 N N-Z titles New page: Nano Lett Nanotechnology Nat Biotechnol Nat Cell Biol Nat Chem Biol Nat Genet Nat Immunol Nat Med Nat Med (Tokyo) Nat Methods Nat Neurosci Nat Protoc Nat Rev Drug Discov Nat Rev Genet Nat ...
- 17:33, 3 February 2010 diff hist +34 Journals
- 16:54, 3 February 2010 diff hist +227 Journals
- 16:08, 3 February 2010 diff hist +107 Ontology Annotator
- 15:46, 3 February 2010 diff hist +20 Ontology Annotator
- 15:44, 3 February 2010 diff hist -1 Ontology Annotator
- 15:43, 3 February 2010 diff hist +45 Ontology Annotator
- 15:42, 3 February 2010 diff hist +12 Ontology Annotator
- 15:40, 3 February 2010 diff hist +3 Ontology Annotator
- 15:40, 3 February 2010 diff hist +284 Ontology Annotator
- 14:57, 28 January 2010 diff hist +256 Ontology Annotator →Wish List, Jan-Feb 2010
- 10:41, 26 January 2010 diff hist 0 In book
- 14:23, 22 January 2010 diff hist +81 In book
- 14:23, 22 January 2010 diff hist +82 In book
- 12:30, 20 January 2010 diff hist -6 New Paper Model - Model and Changes to Pipeline
- 12:30, 20 January 2010 diff hist 0 Paper Pipeline
- 18:27, 19 January 2010 diff hist -108 New Paper Model - Model and Changes to Pipeline
- 18:24, 19 January 2010 diff hist -4 New Paper Model - Model and Changes to Pipeline
- 18:21, 19 January 2010 diff hist +85 New Paper Model - Model and Changes to Pipeline
- 18:19, 19 January 2010 diff hist +49 New Paper Model - Model and Changes to Pipeline
- 18:16, 19 January 2010 diff hist -1 New Paper Model - Model and Changes to Pipeline
- 18:07, 19 January 2010 diff hist +83 New Paper Model - Model and Changes to Pipeline
- 17:58, 19 January 2010 diff hist +1 New Paper Model - Model and Changes to Pipeline
- 17:57, 19 January 2010 diff hist +64 New Paper Model - Model and Changes to Pipeline
- 17:56, 19 January 2010 diff hist +3 New Paper Model - Model and Changes to Pipeline
- 17:56, 19 January 2010 diff hist -1 New Paper Model - Model and Changes to Pipeline
- 17:56, 19 January 2010 diff hist +11 New Paper Model - Model and Changes to Pipeline
- 17:55, 19 January 2010 diff hist +5 New Paper Model - Model and Changes to Pipeline
- 17:54, 19 January 2010 diff hist +4,735 New Paper Model - Model and Changes to Pipeline
- 15:36, 5 January 2010 diff hist +34 Paper Pipeline
- 15:21, 5 January 2010 diff hist +40 Abstracts
- 15:20, 5 January 2010 diff hist +69 Associating genes with papers
- 15:13, 5 January 2010 diff hist +2 What to do about non-standard nomenclature current
- 15:13, 5 January 2010 diff hist +167 N What to do about non-standard nomenclature New page: HMMs? But then what? Either check a synonym list or funnel to a curator for manual checking. Back to Associating genes with papers Back to Paper Pipeline
- 15:12, 5 January 2010 diff hist +49 Associating genes with papers
- 15:11, 5 January 2010 diff hist +40 Abstracts
- 13:38, 5 January 2010 diff hist +7 Abstracts
- 13:33, 5 January 2010 diff hist +93 N What to do about new gene names not yet in WB New page: Look for cosmid names. Back to Associating genes with papers Back to Paper Pipeline current
- 12:29, 5 January 2010 diff hist +36 Abstracts
- 12:24, 5 January 2010 diff hist +182 What to do about large-scale papers current
- 12:17, 5 January 2010 diff hist +33 What to do about large-scale papers
- 12:13, 5 January 2010 diff hist +28 Using the Paper Editor
- 12:13, 5 January 2010 diff hist +37 N Using the Paper Editor New page: WBPaper00030839 - empty gene objects?
- 12:13, 5 January 2010 diff hist +18 Paper Pipeline
- 12:09, 5 January 2010 diff hist +9 Abstracts
- 12:08, 5 January 2010 diff hist +182 Abstracts
- 11:48, 5 January 2010 diff hist +3 Abstracts
- 11:48, 5 January 2010 diff hist +21 Abstracts
- 11:37, 5 January 2010 diff hist +52 Abstracts
- 11:22, 5 January 2010 diff hist +39 Associating genes with papers
- 11:19, 5 January 2010 diff hist +20 Abstracts
- 11:19, 5 January 2010 diff hist +27 Associating genes with papers
- 19:03, 4 January 2010 diff hist +51 Associating genes with papers
- 19:02, 4 January 2010 diff hist +34 Abstracts
- 19:01, 4 January 2010 diff hist +3 Abstracts
- 19:01, 4 January 2010 diff hist +65 Abstracts
- 18:58, 4 January 2010 diff hist -3 Abstracts
- 18:57, 4 January 2010 diff hist +128 Abstracts
- 18:44, 4 January 2010 diff hist +81 Abstracts
- 18:41, 4 January 2010 diff hist +71 What to do about large-scale papers
- 18:41, 4 January 2010 diff hist +57 N What to do about large-scale papers New page: Previously defined as papers that study 50 or more genes.
- 18:40, 4 January 2010 diff hist +90 Associating genes with papers
- 18:34, 4 January 2010 diff hist +40 Associating genes with papers
- 18:33, 4 January 2010 diff hist +21 Abstracts
- 18:31, 4 January 2010 diff hist +1 Associating genes with papers
- 18:31, 4 January 2010 diff hist +109 Associating genes with papers
- 18:28, 4 January 2010 diff hist +1 Abstracts
- 18:27, 4 January 2010 diff hist +42 Abstracts
- 18:27, 4 January 2010 diff hist 0 Associating genes with papers
- 18:27, 4 January 2010 diff hist +28 Associating genes with papers
- 18:26, 4 January 2010 diff hist +43 Associating genes with papers
- 18:26, 4 January 2010 diff hist +2 Abstracts
- 18:26, 4 January 2010 diff hist +321 Abstracts
- 18:20, 4 January 2010 diff hist +157 N Abstracts New page: Currently, genes or proteins mentioned in the abstracts get associated with papers. (This was not always the case.) Are abstracts enough? Here's the data:
- 18:16, 4 January 2010 diff hist +307 N Associating genes with papers New page: Several possible strategies to test, may differ for sectioned vs non-sectioned papers: #Abstracts #Gene frequency #Genes in Results (or equivalent) #[[Gene frequency in Result...
- 18:13, 4 January 2010 diff hist +35 Paper Pipeline
- 13:00, 23 December 2009 diff hist +54 Paper Pipeline
- 14:57, 21 December 2009 diff hist +104 Adding Papers not in PubMed
- 14:45, 21 December 2009 diff hist +134 Adding Papers not in PubMed
- 14:26, 21 December 2009 diff hist +35 Adding Papers not in PubMed
- 14:05, 21 December 2009 diff hist +21 Adding Papers not in PubMed
- 13:56, 21 December 2009 diff hist +100 Adding Papers not in PubMed
- 13:30, 21 December 2009 diff hist +1,123 N Adding Papers not in PubMed New page: New paper information can be entered through the paper editor, but you have to create the paper (i.e. get a WBPaper ID) through postgres first. To do this, you will need to login to tazen...
- 13:21, 21 December 2009 diff hist +33 Paper Pipeline
- 14:26, 16 December 2009 diff hist -14 Primary data Tag
- 14:26, 16 December 2009 diff hist -2 Primary data Tag
- 14:26, 16 December 2009 diff hist +95 Primary data Tag
- 14:25, 16 December 2009 diff hist +28 Primary data Tag
- 14:24, 16 December 2009 diff hist +214 Primary data Tag
- 14:16, 16 December 2009 diff hist +200 N Primary data Tag New page: Paper Types that will get Primary Data Tag: Paper Types that will get No Primary Data Tag: Paper Types that will get Not Designated Tag: Back to [[New Paper Model - Model and Changes t...
- 14:14, 16 December 2009 diff hist +22 New Paper Model - Model and Changes to Pipeline
- 13:38, 16 December 2009 diff hist +337 Project meeting agendas and minutes
- 18:51, 9 December 2009 diff hist +115 In book
- 18:50, 9 December 2009 diff hist +114 In book
- 17:33, 9 December 2009 diff hist -434 In book
- 17:32, 9 December 2009 diff hist +10,968 In book
- 16:13, 9 December 2009 diff hist +115 Type - mapping incoming Type
- 16:12, 9 December 2009 diff hist +63 Type - mapping incoming Type
- 16:10, 9 December 2009 diff hist +1,675 N Type - mapping incoming Type New page: Nearly all articles are assigned the Type Journal Article when they first appear in PubMed. Note that in PubMed, the Type is not always case sensitive; they have JOURNAL ARTICLE and Journa...
- 13:56, 9 December 2009 diff hist +123 Type - mapping of current to future Type
- 13:53, 9 December 2009 diff hist +1,336 N Type - mapping of current to future Type New page: '''Mapping of current ?Paper Type to new ?Paper Type:''' Note: all ?Paper Types are listed, even if there is no change to the text. However, new or changed Types are in '''bold''', with ...
- 13:53, 9 December 2009 diff hist +70 New Paper Model - Model and Changes to Pipeline
- 13:51, 9 December 2009 diff hist +18 Type
- 13:51, 9 December 2009 diff hist -3 Type
- 13:50, 9 December 2009 diff hist +1,321 N Type New page: '''Mapping of current ?Paper Type to new ?Paper Type:''' Note: all ?Paper Types are listed, even if there is no change to the text. However, new or changed Types are in '''bold''', with ...
- 16:10, 8 December 2009 diff hist +23 WormBase SVMs →seqchange and genesymbol
- 13:07, 8 December 2009 diff hist +28 WormBase
- 13:07, 8 December 2009 diff hist +1,543 WormBase
- 19:32, 7 December 2009 diff hist +456 Random Selection of New Training Set Papers
- 18:53, 7 December 2009 diff hist -5 Training Set
- 18:52, 7 December 2009 diff hist +10 Training Set
- 18:52, 7 December 2009 diff hist +57 Training Set
- 18:51, 7 December 2009 diff hist +27 Random Selection of New Training Set Papers
- 18:47, 7 December 2009 diff hist +134 Random Selection of New Training Set Papers
- 17:13, 7 December 2009 diff hist +553 N Random Selection of New Training Set Papers New page: Checking a random list of training set papers to verify quality for SVM: 'Yes' means the paper has the data we'd want for training. WBPaper00032217 - yes WBPaper00032287 - yes WBPaper0...
- 16:28, 7 December 2009 diff hist +6 Training Set
- 16:28, 7 December 2009 diff hist +6 Training Set
- 16:26, 7 December 2009 diff hist +246 Training Set
- 16:18, 7 December 2009 diff hist -26 WormBase SVMs
- 16:18, 7 December 2009 diff hist +1 112009 seqchange
- 16:17, 7 December 2009 diff hist +74 100209 seqchange
- 16:14, 7 December 2009 diff hist +1 100209 seqchange
- 16:14, 7 December 2009 diff hist +20 100209 seqchange
- 16:13, 7 December 2009 diff hist +49 100209 seqchange
- 16:08, 7 December 2009 diff hist 0 100209 seqchange
- 16:07, 7 December 2009 diff hist +139 100209 seqchange
- 16:07, 7 December 2009 diff hist -1 100209 seqchange
- 16:06, 7 December 2009 diff hist +2 100209 seqchange
- 16:05, 7 December 2009 diff hist +965 100209 seqchange
- 14:45, 7 December 2009 diff hist +79 100209 seqchange
- 14:44, 7 December 2009 diff hist +830 N 100209 seqchange New page: {| class="wikitable" border="1" |- ! WBPaper ID ! SVM confidence ! True positive for seqchange? ! True positive for genesymbol? ! Comments |- ! WBPaper00035194 ! high ! Sort of ! No ! Disc...
- 14:10, 7 December 2009 diff hist +25 WormBase SVMs →seqchange and genesymbol
- 14:00, 7 December 2009 diff hist -2 WormBase SVMs →seqchange and genesymbol
- 14:00, 7 December 2009 diff hist -5 WormBase SVMs →seqchange and genesymbol
- 18:04, 4 December 2009 diff hist -4 XML Status Tag
- 18:04, 4 December 2009 diff hist +243 XML Status Tag
- 18:01, 4 December 2009 diff hist +1,520 N XML Status Tag New page: '''For checking the indexing status of a paper in PubMed, we need to check the Status tag at the beginning of the record:''' Partial XML for an '''indexed''' paper, Status=MEDLINE <...
- 17:55, 4 December 2009 diff hist +20 New Paper Model - Model and Changes to Pipeline
- 14:42, 4 December 2009 diff hist +4 Overall performance
- 14:41, 4 December 2009 diff hist +7 Overall performance
- 14:41, 4 December 2009 diff hist +54 Overall performance
- 14:37, 4 December 2009 diff hist +27 Overall performance
- 14:35, 4 December 2009 diff hist +574 Overall performance
- 14:28, 4 December 2009 diff hist +11 Overall performance
- 14:27, 4 December 2009 diff hist -1 Overall performance
- 14:26, 4 December 2009 diff hist +3 Overall performance
- 14:26, 4 December 2009 diff hist +330 Overall performance
- 12:49, 4 December 2009 diff hist +43 Overall performance
- 12:48, 4 December 2009 diff hist -12 Overall performance
- 12:48, 4 December 2009 diff hist -3 Overall performance
- 12:46, 4 December 2009 diff hist +1,488 N Overall performance New page: {| border="1" |- ! Date ! Paper - SVM Positive ! Confidence Score ! True Positive (strict) ! True Positive - seqchange (more lenient) ! Comment |- ! 103009 ! WBPaper00035315 ! high ! Y...
- 12:30, 4 December 2009 diff hist +1 Training Set
- 12:30, 4 December 2009 diff hist +25 Training Set
- 12:26, 4 December 2009 diff hist +2 Training Set
- 12:26, 4 December 2009 diff hist +785 Training Set
- 12:19, 4 December 2009 diff hist -108 Training Set
- 12:18, 4 December 2009 diff hist +19 Training Set
- 12:17, 4 December 2009 diff hist +191 Training Set
- 12:14, 4 December 2009 diff hist +37 Training Set
- 12:14, 4 December 2009 diff hist +318 N Training Set New page: 09/17/209 email: seqchange is highlighted in yellow, which means that the SVM performance is good judging by using those papers fristpassed. I need to obtain a list of curated paper IDs ...
- 18:57, 3 December 2009 diff hist +53 WormBase SVMs →seqchange and genesymbol
- 18:51, 3 December 2009 diff hist +44 WormBase SVMs →seqchange and genesymbol
- 18:50, 3 December 2009 diff hist +44 WormBase SVMs →geneprod_GO
- 12:05, 3 December 2009 diff hist +1 New Paper Model - Model and Changes to Pipeline
- 12:03, 3 December 2009 diff hist -1 New Paper Model - Model and Changes to Pipeline
- 12:02, 3 December 2009 diff hist +7 New Paper Model - Model and Changes to Pipeline
- 12:01, 3 December 2009 diff hist -3 New Paper Model - Model and Changes to Pipeline
- 11:52, 3 December 2009 diff hist +93 New Paper Model - Model and Changes to Pipeline
- 12:40, 1 December 2009 diff hist +31 Paper Pipeline
- 16:11, 30 November 2009 diff hist -1 (4 papers)
- 16:10, 30 November 2009 diff hist +3 (4 papers)
- 16:10, 30 November 2009 diff hist +120 (4 papers)
- 16:05, 30 November 2009 diff hist +1,217 N (4 papers) New page: '''Papers flagged by authors for structcorr''' {| border="1" |- ! WBPaper ID ! Author comments (checked means the author flagged the data type but left no additional comments) ! Date the ...
- 15:58, 30 November 2009 diff hist +2 (11 papers)
- 15:58, 30 November 2009 diff hist -2 (11 papers)
- 15:57, 30 November 2009 diff hist +653 (11 papers)
- 15:51, 30 November 2009 diff hist +8 (11 papers)
- 15:50, 30 November 2009 diff hist -67 (11 papers)
- 15:47, 30 November 2009 diff hist +175 (11 papers)
- 15:45, 30 November 2009 diff hist +4 (11 papers)
- 15:44, 30 November 2009 diff hist +390 (11 papers)
- 15:23, 30 November 2009 diff hist -6 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:23, 30 November 2009 diff hist +17 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:22, 30 November 2009 diff hist +1 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:22, 30 November 2009 diff hist +71 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:21, 30 November 2009 diff hist -1 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:21, 30 November 2009 diff hist +1 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:20, 30 November 2009 diff hist +71 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:20, 30 November 2009 diff hist +3 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:17, 30 November 2009 diff hist +59 November 25, 2009 - Sequence Curation Flags →Action Items
- 15:12, 30 November 2009 diff hist +1 November 25, 2009 - Sequence Curation Flags
- 15:12, 30 November 2009 diff hist +35 November 25, 2009 - Sequence Curation Flags