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- #[[2010 - Paper Pipeline: Documentation and Instructions]] #[[New Paper Model - Model and Changes to Pipeline]]1 KB (130 words) - 21:21, 15 March 2021
- ...CC, I'd initially just searched through all paper types, but removing some paper types from the searches would more accurately reflect the real curation pip ...I don't really know what types of papers are included in some of the other paper types like COMMENT and LETTERS, so it'd be good to know so I can make a bet2 KB (259 words) - 18:08, 16 August 2010
- ! [http://dev.wormbase.org/db/misc/paper?name=WBPaper00035124;class=Paper 00035124] .../wiki/index.php/November_25%2C_2009_-_Sequence_Curation_Flags#Action_Items Paper List]473 bytes (68 words) - 18:50, 10 August 2010
- #REDIRECT [[Using the Paper Editor]]36 bytes (5 words) - 21:39, 8 May 2011
- We have several options for making gene-paper associations: ...iates genes and proteins mentioned in paper and meeting abstracts with the paper object in postgres. Note that the script was only recently updated (Octobe1 KB (164 words) - 23:35, 14 February 2011
- The paper editor is accessible either from the curation index page (click on the seco '''Might be helpful to reorganize the index page, to put all of the paper-related forms together. We could keep the link to the old editor, but make7 KB (1,204 words) - 18:58, 30 June 2014
- // ?Paper class - krb 040223 // ?Paper class - krb 0402235 KB (471 words) - 16:07, 4 October 2010
- Back to [[Paper Pipeline]]71 bytes (11 words) - 21:51, 11 May 2011
- ...from the journal itself. An e-mail alert is sent to WB QC curators that a paper has been approved and has entered the pipeline. ...11/20/09) or WBPaperIDs were getting mixed up (see e-mail from 1/15/10) or paper information was not getting entered properly (see e-mails 2/15/10, 2/16/11)3 KB (455 words) - 22:01, 16 May 2011
- = Methods & Approaches for Paper Categorization =10 KB (1,279 words) - 18:20, 18 October 2013
- 90 bytes (15 words) - 13:16, 5 November 2018
- =PMID Downloads and Paper Editor= ...re dumping the papers file, double-check the 'Find Dead Genes' list on the paper editor and make any necessary updates.2 KB (320 words) - 20:59, 12 May 2017
- =Approving Papers through the Paper Editor= ...c.cgi/wormbase/wspec/models.wrm?root=ensembl&view=log as specified in the ?Paper model] in WormBase.3 KB (403 words) - 16:02, 27 March 2019
- [http://dev.wormbase.org/db/misc/paper?name=WBPaper00004402;class=Paper WBPaper00004402] Ahringer, Chromosome I RNAi screen [http://dev.wormbase.org/db/misc/paper?name=WBPaper00004402;class=Paper WBPaper00004403] Gonczy, Chromosome III RNAi cell division screen2 KB (313 words) - 18:20, 16 August 2010
- Back to [[Paper Pipeline]] =List of Paper Tables in Postgres (Alphabetical)=25 KB (3,238 words) - 16:42, 8 November 2019
- ...put paper titles from a list of input paper IDs. The tool accepts WormBase Paper IDs (e.g. WBPaper00012345), PubMed IDs (pmid12345678) or digital object ide ...they would like to see, including WBPaper ID, PubMed ID (pmid), DOI and/or paper title. For example, a series of WBPaper IDs may be entered like this:1 KB (265 words) - 21:02, 11 March 2015
- '''Correct invalid PMIDs and their associated paper types - Kimberly''' ...t.cgi if check if a DOI already exists in wpa_identifier, don't create new paper then, just the afp_passwd. -- DONE7 KB (1,103 words) - 18:08, 16 August 2010
- * Remove redundant gene-paper associations Not sure how this is generated; I believe this was done before my time as paper curator.4 KB (556 words) - 12:45, 21 May 2019
- Back to [[Paper Pipeline]] =Paper Pipeline Documentation=412 bytes (47 words) - 15:19, 15 April 2011
- '''Instructions for adding a PMID identifier to a Paper Object''' ...indexed for MEDLINE, but we don't have the PMID, you can add it using the paper editor.2 KB (381 words) - 16:53, 2 November 2010
- #[[Gene-Paper Connections]] #[[Genetics Paper Pipeline]]388 bytes (49 words) - 20:02, 15 April 2011
- '''Example 1: Paper describes cloning of a new gene, epg-8:''' Data in the paper/objects to curate:2 KB (308 words) - 10:39, 30 March 2011
- Back to [[Paper Pipeline]] History Merged_into UNIQUE ?Paper XREF Acquires_merge10 KB (928 words) - 18:34, 2 May 2011
Page text matches
- ...rmbase.org/wiki/index.php/New_Paper_Model_-_Model_and_Changes_to_Pipeline Paper Model Changes] '''For checking the indexing status of a paper in PubMed, we need to check the Status tag at the beginning of the record:'2 KB (155 words) - 18:26, 4 December 2009
- #[[2010 - Paper Pipeline: Documentation and Instructions]] #[[New Paper Model - Model and Changes to Pipeline]]1 KB (130 words) - 21:21, 15 March 2021
- Paper Types that will get '''Primary Data Tag''' (these types will only have a si Paper Types that will get '''No Primary Data Tag''':856 bytes (106 words) - 18:22, 16 August 2010
- #[[Gene-Paper Connections]] #[[Genetics Paper Pipeline]]388 bytes (49 words) - 20:02, 15 April 2011
- '''Adding Missing Authors to a Paper''' If authors are missing from a paper object, they can be added by clicking on the edit box to the right of the a588 bytes (110 words) - 18:55, 3 March 2011
- This is fixed for when the paper is approved and brought into postgres, but not for the display on the edito Back to [[Paper Pipeline]]156 bytes (28 words) - 13:41, 12 May 2011
- Back to [[Paper Pipeline]] =Paper Pipeline Documentation=412 bytes (47 words) - 15:19, 15 April 2011
- ...ences and one evidence was valid while another was invalid, the valid gene-paper connection was transferred even if the invalid connection was actually corr This resulted in a resurfacing of dead gene-paper connections for the WS213 build.2 KB (279 words) - 18:55, 16 August 2010
- === Molecule class to paper class connectivity === Reference ?Paper XREF Molecule587 bytes (86 words) - 10:07, 28 November 2012
- ...id PMID. For this reason, I haven't approved corrections or errata in the paper editor. It would, I think, be good to have corrections and errata in the WB paper collection, though, but if we want them we'll need to develop a new pipelin1,004 bytes (161 words) - 20:09, 15 April 2011
- '''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 or1 KB (205 words) - 17:49, 17 August 2010
- We have several options for making gene-paper associations: ...iates genes and proteins mentioned in paper and meeting abstracts with the paper object in postgres. Note that the script was only recently updated (Octobe1 KB (164 words) - 23:35, 14 February 2011
- === WB Genetics Paper - Submission Monday, December 11th === ...m WormBase to the Alliance. Still more a planning document than a finished paper. '''Everyone should check the document and add things to be discussed, para1 KB (159 words) - 18:22, 7 December 2023
- ...om a paper object. This doesn't happen often and usually applies to older paper entries. ...w that you need to delete these authors. She will also need to remove any paper-person connections from the entry.1 KB (234 words) - 15:30, 15 April 2011
- '''Background:''' When we started using the new Paper Types, we included a new Type, Book. In the ?Paper model, books and book chapters are related to one another by the Contains a372 bytes (60 words) - 20:54, 10 August 2010
- === Paper ===944 bytes (131 words) - 20:41, 13 August 2010
- * Paper retraction134 bytes (16 words) - 11:57, 2 January 2020
- '''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 or1 KB (183 words) - 17:49, 17 August 2010
- ...put paper titles from a list of input paper IDs. The tool accepts WormBase Paper IDs (e.g. WBPaper00012345), PubMed IDs (pmid12345678) or digital object ide ...they would like to see, including WBPaper ID, PubMed ID (pmid), DOI and/or paper title. For example, a series of WBPaper IDs may be entered like this:1 KB (265 words) - 21:02, 11 March 2015
- *Issue #8907: WBPaper00063926 has no title in ACeDB. The paper title exists in postgres but not in ACeDB. In WS287, there are 8 papers fro <br>Paper : "WBPaper00062581"2 KB (348 words) - 17:52, 2 February 2023
- ...CC, I'd initially just searched through all paper types, but removing some paper types from the searches would more accurately reflect the real curation pip ...I don't really know what types of papers are included in some of the other paper types like COMMENT and LETTERS, so it'd be good to know so I can make a bet2 KB (259 words) - 18:08, 16 August 2010
- Once a paper has been entered into Postgres if it has not been labeled as "review" or "f ...ment is available for a curator to access. It also remains grey until the paper has been through Textpresso (?).3 KB (561 words) - 21:38, 15 August 2013
- Back to [[Paper Pipeline]]71 bytes (11 words) - 21:51, 11 May 2011
- ...'' When papers are entered manually, is there a script that associates the paper with genes mentioned in the abstract? ...mation can be entered through the paper editor, but you have to create the paper (i.e. get a WBPaper ID) through postgres first.2 KB (247 words) - 19:37, 19 November 2010
- =Approving Papers through the Paper Editor= ...c.cgi/wormbase/wspec/models.wrm?root=ensembl&view=log as specified in the ?Paper model] in WormBase.3 KB (403 words) - 16:02, 27 March 2019
- // connects to condition and paper objects Reference ?Paper XREF SAGE_experiment543 bytes (47 words) - 09:05, 5 October 2010
- ! Paper - SVM Positive ! Fig. S7 shows molecular nature of deps-1 alleles, but not sequenced in this paper.2 KB (301 words) - 18:05, 16 August 2010
- ==Paper Tables== ==Paper Editor==4 KB (536 words) - 20:31, 25 April 2011
- **Paper Type ...ssociated with a Paper_type, a unique text string designating what type of paper this is, e.g. ARTICLE, REVIEW, COMMENTARY, etc.2 KB (240 words) - 17:41, 16 August 2010
- Back to [[Paper Pipeline]]93 bytes (14 words) - 13:33, 5 January 2010
- Back to [[Entering New Paper Objects]]151 bytes (24 words) - 15:41, 8 April 2010
- // ?Paper class - krb 040223 // ?Paper class - krb 0402235 KB (471 words) - 16:07, 4 October 2010
- Paper ?Paper715 bytes (81 words) - 11:06, 10 August 2010
- Takes postgres paper entries '''missing''' author, pages, title, type and year and checks PudMed169 bytes (25 words) - 10:51, 21 July 2009
- Back to [[Paper Pipeline]]169 bytes (27 words) - 15:13, 5 January 2010
- Publication Paper ?Paper XREF Person #Evidence Not_paper ?Paper XREF Not_person #Evidence3 KB (272 words) - 16:10, 4 October 2010
- '''Example 1: Paper describes cloning of a new gene, epg-8:''' Data in the paper/objects to curate:2 KB (308 words) - 10:39, 30 March 2011
- [[Paper Pipeline]] ...ill acquire a merge (and get an Acquires_merge tag in the .ace file) and a paper that is being merged into another (will get a Merged_into tag in the .ace f5 KB (837 words) - 17:43, 16 August 2010
- Reference ?Paper XREF Describes_analysis ...XREF Conducted // not always the same as the author of the paper - eg Erich running OrthoMCL1 KB (104 words) - 10:38, 10 August 2010
- ...'GAF' dumped from postgres in the files that need to be compared for gene-paper connections. *The postgres file could just be a file of gene-paper connections for all 'P' annotations. This file would include all annotatio674 bytes (110 words) - 19:07, 5 November 2014
- ...op of the script, there is a list that maps postgres paper table names to ?Paper model tag names. ***Paper types are indicated using an index table, pap_type_index. Same also for pa2 KB (329 words) - 15:21, 7 August 2014
- ***When a paper is reviewed, one of three things can happen. It is: ...ted in the [http://tazendra.caltech.edu/~postgres/cgi-bin/paper_editor.cgi Paper Editor]3 KB (446 words) - 16:01, 1 July 2014
- "Paper" tag becomes "Reference"166 bytes (25 words) - 15:02, 5 March 2011
- With the move to the new paper editor, the instructions on this page are now obsolete. =First-Pass a paper=4 KB (751 words) - 23:40, 13 August 2010
- ...from the journal itself. An e-mail alert is sent to WB QC curators that a paper has been approved and has entered the pipeline. ...11/20/09) or WBPaperIDs were getting mixed up (see e-mail from 1/15/10) or paper information was not getting entered properly (see e-mails 2/15/10, 2/16/11)3 KB (455 words) - 22:01, 16 May 2011
- Back to [[Entering New Paper Objects]]174 bytes (26 words) - 23:17, 13 August 2010
- ...cceptance of the paper by GENETICS and through to the incorporation of the paper into WB.<br> Genetics (1) The paper gets accepted.3 KB (471 words) - 19:53, 19 April 2012
- * Generally, each reference (paper) gets its own line in the GAF * Sometimes GO annotations do not have a paper, and so use a different reference object, method2 KB (344 words) - 16:30, 3 April 2014
- *Ability to toggle entire Paper (to hide) and sections of paper (already exists but is not working properly) '''Done''' ...hat loads the sentences more frequently placed, in front of each different paper '''Done. You can have as many buttons as you want, but you can only have o1 KB (246 words) - 04:38, 13 October 2010
- *Paper uses GO annotation for C. elegans GPCRs to identify receptors, and their hu310 bytes (43 words) - 19:43, 29 February 2016
- ...dies||abp_ ||Daniela Raciti||find Antibody<br>Paper with Antibody<br>Total Paper--Antibody links|||| ...br>#new papers curated for construct <br> average # constructs curated/new paper||4 KB (580 words) - 18:13, 6 October 2017
- Back to [[Paper Pipeline]]343 bytes (52 words) - 12:24, 5 January 2010
- #[Transgene/Summary/Paper Connections]313 bytes (41 words) - 20:45, 24 September 2010
- // Summary records the whole description extracted from paper // Other_name holds the antibody's name appeared in the paper, such as MH273 KB (318 words) - 00:53, 7 December 2010
- Back to [[Paper Pipeline]] since the objects are associated with the original paper, WBPaper00004137. I don't know who2 KB (248 words) - 22:57, 13 August 2010
- *[[Gene-Paper Associations]] *[[Paper Pipeline]]3 KB (325 words) - 17:36, 25 April 2023
- 2. Manually via author-paper verification Back to [[Paper Pipeline]]1,002 bytes (141 words) - 23:09, 30 April 2011
- Back to [[Paper Pipeline]] History Merged_into UNIQUE ?Paper XREF Acquires_merge10 KB (928 words) - 18:34, 2 May 2011
- AGR Paper - soft deadline for edits is this Friday, but some modifications can be mad ...m WormBase to the Alliance. Still more a planning document than a finished paper. Everyone should check the document and add things to be discussed, paragra2 KB (267 words) - 17:43, 16 November 2023
- == NAR paper == ...point person/representative; three representatives coordinate writing the paper and act as first authors?2 KB (378 words) - 16:32, 3 August 2017
- *Discussion of allele-paper connections **Alleles get associated with a paper if there is phenotypic or molecular data3 KB (407 words) - 01:16, 19 February 2011
- * New ?Paper Type for WS271 MODELS395 bytes (55 words) - 11:59, 15 April 2019
- ...rently there wasn’t one for the RGD or WormBase paper. So someone on that paper will need to submit to PMC. ...straightforward. Is there someone in your group who can do that for this paper?1 KB (241 words) - 18:19, 7 February 2019
- '''Instructions for adding a PMID identifier to a Paper Object''' ...indexed for MEDLINE, but we don't have the PMID, you can add it using the paper editor.2 KB (381 words) - 16:53, 2 November 2010
- Reference ?Paper XREF Rnaseq_library // add this to ?Paper3 KB (252 words) - 16:46, 9 January 2014
- ...so maybe that's why it was removed. In the other, it's not clear why the paper is not included. '''Paper is valid but has a new PMID'''3 KB (444 words) - 23:42, 13 August 2010
- The paper editor is accessible either from the curation index page (click on the seco '''Might be helpful to reorganize the index page, to put all of the paper-related forms together. We could keep the link to the old editor, but make7 KB (1,204 words) - 18:58, 30 June 2014
- ! Paper discussed mRNA sequences bound to protein. The term 'sequence' in various ! This paper used a lot of plasmid constructs and talked about promoter sequences.2 KB (272 words) - 18:58, 10 August 2010
- Back to [[Paper Pipeline]]375 bytes (57 words) - 13:44, 12 May 2011
- ?Paper > Reference ?Paper XREF Picture3 KB (354 words) - 11:08, 3 December 2010
- == Genetics paper == Sian Gramates - coordinating the FlyBase paper2 KB (298 words) - 16:32, 5 August 2021
- * Remove redundant gene-paper associations Not sure how this is generated; I believe this was done before my time as paper curator.4 KB (556 words) - 12:45, 21 May 2019
- # '''Add Zotero support to the Paper page; others? CiteULike? Endnote? Mendely?''' ===Paper===2 KB (275 words) - 15:30, 11 January 2011
- ! [http://dev.wormbase.org/db/misc/paper?name=WBPaper00035124;class=Paper 00035124] .../wiki/index.php/November_25%2C_2009_-_Sequence_Curation_Flags#Action_Items Paper List]473 bytes (68 words) - 18:50, 10 August 2010
- Reference ?Paper XREF Expression_cluster //reference of the experiment Expr_pattern - this is actually used by one paper regarding Localizome.2 KB (177 words) - 22:50, 6 December 2010
- ! [http://dev.wormbase.org/db/misc/paper?name=WBPaper00031858;class=Paper 00031858] ! [http://dev.wormbase.org/db/misc/paper?name=WBPaper00035125;class=Paper 00035125]2 KB (281 words) - 18:56, 10 August 2010
- ** During the call earlier we talked about the ?Paper model having *** Author ?Author XREF Paper #Affiliation3 KB (492 words) - 18:48, 17 March 2021
- location of files on Textpresso for retrieving paper titles and abstracts paper identifier mapping file2 KB (204 words) - 19:18, 17 November 2011
- ===='''?Paper'''====2 KB (260 words) - 11:11, 27 July 2012
- == WB Genetics paper update ==2 KB (299 words) - 16:04, 20 May 2021
- === Migrating Paper Pipeline to Alliance === ...-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance2 KB (314 words) - 19:19, 14 December 2021
- ...otations that are NOT present in the gene_association file (i.e., the gene-paper combination exists in the Phenotype2GO file but NOT in the gene_association ...ation, that it will have covered all of the possible annotations from that paper. This may not always be 100% true but, at least for now, it will be simple3 KB (482 words) - 21:21, 7 November 2014
- *Discussion of what features are commonly used in the Caltech paper editor or otherwise wrt papers252 bytes (35 words) - 17:49, 12 May 2022
- '''Correct invalid PMIDs and their associated paper types - Kimberly''' ...t.cgi if check if a DOI already exists in wpa_identifier, don't create new paper then, just the afp_passwd. -- DONE7 KB (1,103 words) - 18:08, 16 August 2010
- ?Reference Reference ?Paper300 bytes (27 words) - 08:59, 5 October 2010
- Reference ?Paper //Paper that defines the condition.2 KB (183 words) - 22:58, 6 December 2010
- ...(2001), PNAS 98, 218-223] (SMD data from Kim laboratory's 2001 microarray paper)476 bytes (62 words) - 21:35, 29 November 2010
- Reference ?Paper XREF WBProcess ...be filtered out during .ace file dumps for those cases where the gene and paper have been connected to the process through other tags, i.e. GO mappings, ph4 KB (503 words) - 00:51, 7 November 2013
- * Have "unpublished" data mentioned in one paper later published in another? Maybe, difficult to know === LinkOut from PubMed paper pages to WormBase paper pages? ===4 KB (544 words) - 16:22, 5 January 2017
- ...added to Arun's object markup list, so new objects can be marked up in the paper along with known WB objects. NOTE: these objects will need to be entered co * populate the postgres table and the corresponding first pass paper curation form used by fp curators6 KB (1,017 words) - 19:34, 2 December 2011
- ==Comments concerning GO linking of this paper== **'midbody' - GO term is wrong for this word in this paper3 KB (511 words) - 21:07, 1 August 2011
- ==Comments concerning GO linking of this paper== ...tissues, so the global linking of all instances of 'aging' throughout this paper is counter to the point the author is trying to make.3 KB (442 words) - 21:09, 1 August 2011
- ...te the yearly NAR paper. We are also looking into creating a more in-depth paper for Genetics.1 KB (211 words) - 17:49, 15 April 2021
- ...f the objects to be classified, in our case words, numbers or phrases in a paper, to identify characteristic features of a particular data type and then use770 bytes (117 words) - 13:08, 20 November 2009
- ! Paper describes chromosome binding in terms of localization.653 bytes (82 words) - 19:01, 10 August 2010
- I need to obtain a list of curated paper IDs to validate the results. ! Ids of curated paper2 KB (241 words) - 17:46, 17 August 2010
- We also hold "curation data", for example the curation status of a paper, separately == WB Paper Data to Alliance ==3 KB (487 words) - 16:36, 18 March 2021
- - More than one paper for Worm? - Should also do an additional paper for new the web-site.1 KB (213 words) - 16:30, 21 July 2011
- ...a table that is a comprehensive display of the curation status of a given paper as well as a table that can show how far we've come along in curating the n ...o_Curation Brief summary of curator first pass pipeline, obsolete with new paper editor]6 KB (841 words) - 08:24, 24 October 2014
- Reference ?Paper //Describes design of the chip726 bytes (57 words) - 14:42, 4 October 2010
- === Hench et al paper === * Thomas Burglin would like the data from paper 00046864 to be included in WB4 KB (572 words) - 17:01, 13 January 2021
- ...cceptance of the paper by GENETICS and through to the incorporation of the paper into WB.<br> Genetics (1) The paper gets accepted.7 KB (1,133 words) - 20:36, 23 July 2013
- * Maybe Cecilia could link a WBPerson as corresponding author for a paper during curation? === Neural Network (NN) Paper Classification Results ===5 KB (873 words) - 14:41, 4 February 2021
- #Paper database code:numerical identifier:Paper section:Sentence ID in Textpresso document:corpus_date_of_search2 KB (261 words) - 17:08, 16 April 2013
- For firstpass, there is an easy way to estimate whether a paper contains Expr_pattern data, which is the purpose of the paper.3 KB (582 words) - 23:08, 13 August 2010
- Reference ?Paper XREF Expr_profile595 bytes (73 words) - 10:27, 4 October 2010
- ...ation_progress] wiki. You can also use this form to assess if a particular paper or a list of papers have been flagged for a given datatype. Use the form to *Manual first pass - from 200? until 2009, one curator manually flagged every paper that was uploaded by WormBase for containing any of over 30 datatypes. Thes7 KB (1,148 words) - 23:02, 23 October 2014
- '''Congratulations on the publication of your paper!'''<br> If your paper contains experiments on C. elegans and related nematodes, please continue w11 KB (1,688 words) - 11:06, 21 December 2011
- * His paper has been submitted and is expected to be accepted soon ==NAR Paper==3 KB (448 words) - 16:04, 5 October 2017
- *Paper ID *Do we also want to store if a paper was used in an SVM training set?5 KB (843 words) - 17:17, 12 October 2012
- Searches would return sentences, one page on the curation form per paper, if possible? #Paper5 KB (764 words) - 21:17, 18 March 2013
- Reference ?Paper XREF Picture1 KB (95 words) - 21:28, 6 December 2010
- == Genetics Paper==2 KB (354 words) - 16:05, 16 September 2021
- =PMID Downloads and Paper Editor= ...re dumping the papers file, double-check the 'Find Dead Genes' list on the paper editor and make any necessary updates.2 KB (320 words) - 20:59, 12 May 2017
- ...next couple months- good to have the model in for this. Will have another paper with males single-cell RNASeq. <br> == WB Paper Data to Alliance ==4 KB (709 words) - 13:27, 5 April 2021
- :paper/email EMPTY :paper/species EMPTY7 KB (604 words) - 18:21, 11 November 2014
- * Paper upload directly from authors - https://github.com/WormBase/website/issues/8 ...We need to decide if that specific patent can be included. We don't have a paper type for patents and they are not peer reviewed (at least the experiments a3 KB (462 words) - 17:47, 4 February 2021
- ** Kimberly will review and clean up any erroneous gene-paper connections ...were to accept a bulk submission from Creative Biolabs, there would be no Paper attached to the record.2 KB (303 words) - 15:59, 4 November 2021
- * Yesterday we (FlyBase, ZFIN, and WormBase) presented paper curation status tracking * Is there a working list of Phenologs anywhere? See Ed Marcotte's paper5 KB (715 words) - 15:49, 4 August 2016
- 'Yes' means the paper has the data we'd want for training; flagged means it was flagged during ma1 KB (159 words) - 18:33, 16 August 2010
- > References ?Paper (optional XREF Species_in_paper) <s>* "paper link missing to sax-1?" help desk email from Nathalie Pujol Sept 26</s><br>3 KB (534 words) - 17:29, 1 October 2020
- *Easy to add the genotype information when a curator is reading the paper, and to do it at the same time as request for the ID371 bytes (63 words) - 02:27, 1 April 2020
- ...data for ''C. elegans'' isolates other than Bristol are presented in this paper." ...per||genestudied||Please list any gene that is a focus of analysis in your paper.16 KB (2,310 words) - 11:05, 21 December 2011
- ...rstpass is to alert curators to the presence of a data type in a published paper. ...e actual data in the paper, saving the data curator time in looking at the paper.6 KB (1,045 words) - 21:14, 24 September 2010
- == Science paper on NHGRI funding ==2 KB (371 words) - 18:38, 17 December 2015
- ...eason there are two classes is that we didn't implement the feature in the paper editor that allowed us to mark these papers as 'for functional annotation o ...t pass curation pipeline. Going forward, any papers marked as such in the paper editor, should be excluded from the Textpresso mark-up and automation pipel2 KB (352 words) - 18:13, 17 August 2010
- *Number of paper-gene connections *Number of paper-RNAi connections2 KB (307 words) - 14:04, 7 February 2013
- ...includes a small geographic map displaying locations of the authors of the paper: $WORMBASE/cgi-perl/misc/paper: CGI script that contains the code segment4 KB (711 words) - 23:25, 13 August 2010
- Reference ?Paper XREF Microarray_experiment892 bytes (72 words) - 14:43, 4 October 2010
- ?Paper700 bytes (98 words) - 09:44, 4 October 2010
- ...d papers to textpresso as we get them into the database each week? For new paper curation it would be good to get papers when published into Textpresso, and633 bytes (113 words) - 17:29, 19 April 2011
- while (my @row = $result->fetchrow) { $deadObjects{paper}{invalid}{"WBPaper$row[0]"} = $row[1]; } ...here are papers,Experimental_model\t"$doid"\t"$species"\tPaper_evidence\t"$paper"10 KB (1,461 words) - 23:06, 27 February 2017
- Reference UNIQUE ?Paper XREF Anatomy_function1 KB (119 words) - 10:41, 10 August 2010
- ...etailed Search option. This expands the search to include full text of all paper and meeting abstracts. SEARCH WITH THE WILD CARD (*) ...ch option allows the user to expand the search to include full text of all paper and meeting abstracts as well as Worm Breeder's Gazette (wbg) articles. For2 KB (399 words) - 18:32, 17 August 2010
- ...for ''C. elegans'' isolates other than N2 (Bristol) are presented in this paper.|| ...per||genestudied||Please list any gene that is a focus of analysis in your paper.||Currently done through textpresso scan of abstract||13 KB (1,960 words) - 11:07, 21 December 2011
- ...ank but has something other than "some comment" show all comments for that paper. Paper-Field, would curators want to be able to enter unlimited entries, and make6 KB (1,024 words) - 23:02, 13 August 2010
- references, and reassured them that the most recent paper will appear references are cited in the new paper.5 KB (800 words) - 10:09, 17 February 2012
- 2. - For each author of each paper not verified YES search: Paper auhor_id Author_name3 KB (435 words) - 20:52, 16 May 2011
- ...t UNIQUE #Evidence //source data, <WSversion> ?Sequence pos1 pos2 Evidence(Paper/person etc. remarks) Defined_by_paper ?Paper XREF Feature #Evidence4 KB (394 words) - 08:39, 16 September 2014
- ...ic file format, with tag:value attributes that are readily parsed into the paper tables (pap_). ...se.pl - this script parses the abstract information into the correpsonding paper tables3 KB (532 words) - 13:33, 31 March 2022
- == NAR paper== Todd: NAR paper was accepted, minor revisions submitted, and will be published in a few wee4 KB (645 words) - 23:43, 3 October 2019
- * paper-by-paper or data-type oriented curation pipeline. Data-type oriented curation is mor2 KB (339 words) - 18:43, 8 April 2016
- ...Reference UNIQUE ?Paper XREF RNAi //[070215 ar2] made reference unique so Paper sort of equates to a Study class for Will S3 KB (312 words) - 15:14, 15 July 2010
- Reference ?Paper XREF Operon1 KB (120 words) - 09:24, 10 August 2010
- *Gene IDs can be found from original paper or data set Paper Categorization5 KB (850 words) - 15:32, 5 September 2013
- ! [http://dev.wormbase.org/db/misc/paper?name=WBPaper00035152;class=Paper 00035152] .../wiki/index.php/November_25%2C_2009_-_Sequence_Curation_Flags#Action_Items Paper List]1 KB (159 words) - 18:57, 10 August 2010
- # Should have paper editor tag-- pubmed_final final # Should have paper editor tag--Status valid13 KB (2,062 words) - 14:01, 4 August 2017
- **External identifiers - which ones? PMIDs, doi's, MOD paper IDs, others? **Paper Exclusion List - user supplied, from external data file, e.g. Gene Ontology6 KB (901 words) - 19:21, 29 November 2011
- ...t object to point to then maybe a better approach is just to reference the paper like this: Null ?Paper6 KB (927 words) - 14:23, 10 August 2017
- Reference ?Paper XREF Life_stage918 bytes (98 words) - 14:04, 4 October 2010
- Reference ?Paper XREF Molecule Reference ?Paper XREF Molecule6 KB (543 words) - 23:29, 15 March 2016
- ...will ensure that subsequent linking out from the form to the paper in the paper editor uses the appropriate curator ID. ...ording to relative rank (i.e., combined sentence score of the HMM for that paper).8 KB (1,272 words) - 21:49, 19 December 2012
- | Paper||Kimberly1 KB (200 words) - 17:59, 6 October 2017
- * Generate a new WBPaper via the Paper Editor here: **Enter new paper9 KB (1,391 words) - 19:47, 19 April 2023
- *Strain to paper association. Does every strain mentioned in the paper need to be connected? e.g. N2, OP50. What about alleles and transgenes used **Note that for gene-paper associations, we try to only associate genes that are studied in some way a3 KB (490 words) - 17:22, 18 June 2020
- Reference ?Paper XREF YH1 KB (139 words) - 09:51, 10 August 2010
- Reference ?Paper XREF Genotype * Disease assertions (and relevant paper connections) will be dumped by the Disease Model Annotation OA5 KB (705 words) - 16:31, 16 June 2020
- *When mark a paper, separate into two different types of genes :stable vs unstable ...single object per pair of genes? One object per instance of evidence (per paper)?4 KB (612 words) - 17:13, 1 December 2011
- ===WormBase Paper Curation charge===3 KB (525 words) - 17:20, 4 April 2024
- ...row as an issue when we start marking up multiple mod entities in the same paper === Consider content for NAR paper ===6 KB (912 words) - 01:40, 15 September 2017
- == Methods Paper ==3 KB (541 words) - 15:58, 20 January 2017
- ! [http://dev.wormbase.org/db/misc/paper?name=WBPaper00034761;class=Paper 00034761] .../wiki/index.php/November_25%2C_2009_-_Sequence_Curation_Flags#Action_Items Paper List]1 KB (193 words) - 18:58, 10 August 2010
- With the move to the new paper editor, the instructions on this page are now obsolete. --kjy 18:03, 29 Jul | align="center" style="background:#f0f0f0;"|'''Paper Section'''17 KB (2,417 words) - 11:04, 21 December 2011
- Reference ?Paper XREF Movie #added Oct2013 DR * Reference -> "mov_paper" WBPaperID paper ontology5 KB (814 words) - 18:48, 17 September 2018
- Reference ?Paper XREF Cell_group2 KB (159 words) - 11:11, 10 August 2010
- *Paper911 bytes (147 words) - 20:11, 9 May 2013
- * [[WormBase Model:Paper|Paper]]4 KB (568 words) - 11:06, 23 May 2011
- Populating dois for WormBase Paper Objects 2) Add dois to newly approved papers in the paper editor3 KB (466 words) - 17:00, 22 July 2014
- Back to [[Paper Pipeline]]986 bytes (140 words) - 19:42, 10 August 2010
- Curators should look for information on new transgenes in the paper and supplementary files. ...transgene already exists in postgres under that name, if so, attached the paper to it).9 KB (1,321 words) - 21:59, 3 May 2020
- ...listing the matching papers that are, in turn, linked to their page in the paper editor *** this is the same as the results of performing a gene search in the paper editor: SELECT joinkey, pap_gene FROM pap_gene WHERE pap_gene = '00014200'3 KB (487 words) - 20:29, 18 March 2019
- Reference ?Paper XREF Strain1 KB (119 words) - 16:43, 11 April 2013
- ...ut to everyone on the GO linking crew. This message includes a link to the paper and to the entity table. <br> ...ither don't quite capture the essence of the entity being discussed in the paper, or are cases where maybe the GO term isn't the best or most informative li13 KB (2,118 words) - 16:51, 20 September 2011
- - One or more [is this correct?] Paper objects are specified as reference.1 KB (143 words) - 21:51, 11 August 2010
- '''Genes studied in this paper: ''' Gene(s) studied in the paper. Postgres character name: ''' genestudied.''' Postgres table: jfp<br> '''''Genes cloned in the paper : ''''' Genes newly identified, named, cloned, reassigned etc. Postgres c12 KB (1,832 words) - 18:43, 11 August 2010
- === NAR Paper === ...ositive or negative, otherwise the paper does not get an AFP flag for that paper6 KB (910 words) - 15:23, 5 October 2017
- ==Micropublication in ?Paper class== *DOIs will be handled as other Paper DOIs are handled -might be formalized (DB_info as per Raymond's suggestion)7 KB (934 words) - 19:56, 27 September 2016
- * Caltech created a parallel PubMed search pipeline and paper editor UI for WormBase Parasite ...e ii)display above CenGen and iii) if we want the L2 dataset from the 2017 paper in a similar format2 KB (370 words) - 16:18, 16 March 2023
- * Paul sent around paper this morning: http://www.nature.com/nature/journal/v527/n7576_supp/full/527 ...e to have a mechanism to update authors on what has been curated for their paper6 KB (926 words) - 16:49, 3 December 2015
- Reference ?Paper XREF Expr_pattern //Paper that the experiments were published.4 KB (497 words) - 22:42, 6 December 2010
- *ER -refers to a camera mount in the paper, not the GO term ...rsensitivity - the GO definition is specific to an immune response. in the paper, it is referring to a response to drug.6 KB (970 words) - 19:52, 2 August 2011
- ...gs of the gene product names or synonyms to IDs and generating a file with paper titles and abstracts for display on the curation form. ...and the pmid_data file that maps PMIDs to MOD paper identifiers as well as paper titles and abstracts.5 KB (817 words) - 15:11, 18 February 2014
- *Paul D. is wrapping up the final round of revisions for the GENETICS paper985 bytes (154 words) - 21:08, 6 January 2022
- 3. SoBa Graph for NAR paper. Raymond will discuss with Sibyl on how to change the display.1 KB (165 words) - 18:42, 15 August 2019
- ...agging - a WB curator flags the paper manually, a curator goes through the paper and enters a check mark or comment for a data type in a curator first-pass ...es or the concurrence of these words/phrases in sentences, etc., to flag a paper as positive for a data type, data are stored in the tfp table; see [http://15 KB (2,589 words) - 16:42, 11 January 2018
- === Adding WormBase-Parasite Paper to the Curation Pipeline (Kimberly) === *Developing new paper editor for Jane and Michael P. to approve parasite papers5 KB (689 words) - 15:35, 7 April 2016
- ...for hlh-34 are incorrect. 4 evidences list AVJ -> the authors of the first paper that describes hlh-34 expression (Cunningham et al, 2012 : http://dx.doi.or === 2021 Genetics paper ===5 KB (670 words) - 16:00, 5 August 2021
- Textpresso scans the paper for an e-mail address based on the '@'. The first e-mail it finds is used a1 KB (196 words) - 19:48, 14 January 2013
- //"Reference" show which paper is the source of the data. Reference ?Paper XREF Gene_regulation //primary article that the data were published5 KB (514 words) - 21:15, 7 December 2010
- * For paper-by-paper curators (vs. datatype-by-datatype) it's difficult to parse papers into dat * All MODS still need paper triage6 KB (910 words) - 16:43, 7 March 2019
- Reference ?Paper XREF WBProcess2 KB (207 words) - 14:11, 4 March 2011
- * Ranjana is still waiting on finalization of the Disease paper flagging pipeline * Juancarlos has implemented a filtering mechanism whereby paper lists in the Curation Status Form (CSF) can be further filtered based on to10 KB (1,664 words) - 17:02, 4 December 2013
- ?Mass_spec_experiment Reference ?Paper XREF Mass_spec_experiment // Describes the experiment2 KB (184 words) - 08:38, 17 August 2010
- =Paper Type and Textpresso Searches= ...se, not all of which are actively curated. Therefore, we can exclude some paper types from the Textpresso curation pipelines. Excluded types may include:17 KB (2,401 words) - 22:36, 29 November 2017
- ...cannot be traced to a specific protein based on the data presented in the paper. This is observed particularly with older papers that describe an 'activit1 KB (178 words) - 00:04, 2 February 2011
- * Data in GAF will point to the 2012 Cell paper as a reference for the Transgenome project ...with it; what if users cannot trace data back to source (by looking up the paper)?8 KB (1,289 words) - 18:11, 10 November 2016
- Paper pipeline for other species *Paper-anatomy term associations in Citace Minus; Raymond will take care of them6 KB (983 words) - 18:02, 12 July 2012
- **1- Gene regulation networks paper **2- Transcriptome paper4 KB (609 words) - 20:57, 3 November 2011
- ...ase.org/wiki/index.php/New_Paper_Model_-_Model_and_Changes_to_Pipeline New Paper Model]2 KB (263 words) - 17:49, 17 August 2010
- Reference ?Paper XREF Cell2 KB (215 words) - 11:09, 10 August 2010
- * As before, request focuses on a single paper, but we've now added extra papers at bottom of email message ...a link for users to click on to indicate that the paper in question (focus paper) has no nematode phenotypes6 KB (906 words) - 15:34, 6 December 2018
- *GSA Editors enter the approved paper doi into the WBPaperID [http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms **The ticketer assigns an official WBPaperID, which is needed to track the paper through WB curation paths17 KB (2,790 words) - 20:50, 10 January 2017
- * Emails (1 per paper) sent (most batches 75 at a time): 3,227 total ** June 17: 1 (1 paper)7 KB (1,062 words) - 14:41, 2 August 2018
- *Mapping spreadsheet fields to WB Paper Model:1 KB (201 words) - 16:34, 15 October 2012
- '''Review dicty Paper Pipeline and Textpressso''' '''Other Options for Paper Download'''3 KB (439 words) - 21:25, 6 November 2012
- ...rently if you are working on one paper/object, and want to switch to a new paper or object, the table is not cleared, all new information is appended --[[Us ...a summary of the number and names of objects associated with a particular paper reference upon hitting the Commit button. --[[User:Jolene|Jolene]] 11:45, 36 KB (1,053 words) - 20:38, 24 September 2010
- ...eriments are listed as a table. Sometimes you will see two tables from one paper, because two PCR products (SMD) or target sequences (Affymetrix) were used1 KB (228 words) - 18:30, 17 August 2010
- *Articles can be read into the development database and checked using the paper editor on mangolassi.caltech.edu ...haven't tested that. The file, at a glance, has one affiliation entry per paper entry -- J Okay, we will need to try adding multiple affiliations in separ5 KB (761 words) - 21:04, 10 February 2012
- * General discussion on DOI handling for micropublications and using the ?Paper model ** So many of the tags were shared (or could be shared) with the ?Paper class10 KB (1,475 words) - 16:57, 5 November 2015
- ...ot part of the save constraint pipeline, if you do not choose a value, the paper will not be included in any status counts. ...all transgenes and summary information for the transgenes curated for that paper. This is mostly necessary when authors do not use standard nomenclature to12 KB (1,991 words) - 23:45, 14 February 2011
- <td>Paper</td> [http://dev.wormbase.org:8023/resources/paper/WBPaper00000031 WBPaper00000031]8 KB (1,190 words) - 23:28, 12 March 2012
- ...dd that information to postgres along with details of indexing; display on paper editor ...here were 997 WBPaper objects that did not have a PMID. We know that some paper objects in WB will likely never have a PMID, for example corrections and er14 KB (2,344 words) - 23:02, 14 December 2011
- * OICR will write NAR paper this year for the Database issue.2 KB (232 words) - 09:58, 2 August 2013
- ...E ?Sequence UNIQUE Int UNIQUE Int UNIQUE Text #Evidence //data provided by paper/submitter/project ...E ?Sequence UNIQUE Int UNIQUE Int UNIQUE Text #Evidence //data provided by paper/submitter/project8 KB (1,073 words) - 15:31, 14 December 2012
- #WBPaper00004663 - added doi in paper editor, will need to dump doi in WB GAF ...per00003666 - rab-11.1 Missing PMID. Action - added PMID to paper in WB paper editor.14 KB (1,928 words) - 19:10, 25 January 2013
- *A search for "SimpleMine" got 1 paper in TPC, 5 papers in the old site. *A search for allele "ev673" in TPC returns no results, but expected paper (PMID:24004945 / WBPaper00044133) returned in old site.4 KB (564 words) - 15:22, 4 April 2019
- '''Field 8 Paper for Exp Mod (dis_paperexpmod):''' <br/ > Obo file to be used: Paper obo <br/ >14 KB (2,085 words) - 20:27, 7 July 2022
- Reference ?Paper XREF DO_term |9 || Paper || Autocomplete obo, multivalue || '''required'''|| WBPaper00038373<br/>WBP8 KB (1,088 words) - 22:59, 29 July 2016
- *Juancarlos: will need to export paper data - Kimberly agrees to try it *Paper data is a better than person, since it's less dependent on other data, but7 KB (1,137 words) - 17:57, 17 November 2016
- *White paper on project1 KB (152 words) - 16:31, 16 June 2017
- - Finished the NAR database paper for WB2 KB (260 words) - 15:45, 16 September 2009
- NAR Paper *Paper due at end of October6 KB (971 words) - 16:24, 6 October 2011
- *One large scale paper omitted from upload *Need to wait until SVM paper accepted before moving those computers5 KB (847 words) - 17:49, 1 March 2012
- *For trial, Most mature dataset? -> from 2007 Nature paper, dosage compensation data2 KB (254 words) - 10:42, 12 August 2009
- * [https://github.com/WormBase/website/issues/6186 paper curation form] - CalTech1 KB (213 words) - 16:56, 15 February 2018
- List of e-mails related to each paper: while curating your paper5 KB (693 words) - 18:45, 2 February 2017
- also, publicizing how many times a given paper is accessed through a link originating from a database Nature Methods paper for specifics)3 KB (564 words) - 19:15, 10 August 2010
- ...an internal WB working group to plan the transition from WB to Alliance. Paper approval and acquisition are the first steps in our curation process and we1 KB (229 words) - 16:05, 15 July 2021
- ...to [https://academic.oup.com/g3journal/article/11/3/jkab022/6121926 their paper]. ...s (and other nematode) species genes in our various gene tables, e.g. obo, paper? Any other species?4 KB (600 words) - 18:40, 2 February 2022
- * There are papers in the WormBase collection that are used as paper evidence for some concise descriptions * Many of these were coming up in the disease paper pipeline6 KB (823 words) - 19:38, 2 January 2014
- ****Contact senior author on a paper to check the quality of data from a paper; experts for a process; prioritize based on who responds to author-first-pa *Including images from microarray expression data directly from paper for now7 KB (1,074 words) - 17:19, 4 October 2012
- ...n. These names are put on an exclusion list, and if the cell exists in the paper, they are manually linked to the correct page. The linking was limited to the authors on the paper only and verified with the WB person curator to make sure the links were ma10 KB (1,696 words) - 17:21, 25 July 2013
- paper x x x -2 KB (243 words) - 20:29, 25 May 2011
- 1. Term info panel (which displays info on the paper object, allele, ontology term etc.) ...ber of alleles/rearrangements/transgenes per paper. Total # of phenotypes/ paper. Total number of object-phenotype connections7 KB (1,075 words) - 21:05, 24 September 2010
- * resubmitted NAR paper1 KB (205 words) - 16:41, 14 October 2009
- ...enable recording of negative connections ie Mr X did NOT contribue to this paper. Added Map_evidence to ?Transgene so that the paper that mapping data is taken from can be attributed6 KB (680 words) - 10:54, 21 December 2011
- * ~1000 papers not flagged as C. elegans, but likely mentioned in body of paper; Kimberly reviewing * Will help to encapsulate the data into one object per experiment in a paper, for example8 KB (1,224 words) - 15:34, 21 July 2016
- | Species of focus in paper ||i.e., ''C. elegans'', ''C. elegans'' other than Bristol, nematodes other ...|''C. elegans'' or other Caenorhabditis studied or newly identified in the paper.5 KB (816 words) - 20:11, 7 September 2011
- Back to [[Paper Pipeline]]1 KB (149 words) - 19:20, 10 August 2010
- *Change our paper-by-paper curation *We can look at the [http://www.biomedcentral.com/1471-2105/7/370 Textpresso paper] and reconvene next week to discuss7 KB (1,059 words) - 15:37, 1 August 2013
- === 2020 WB NAR paper ===5 KB (759 words) - 15:02, 11 September 2019
- * [https://github.com/WormBase/website/issues/4901 This paper g3.114.012351v14/9/1765 should be als...]2 KB (239 words) - 15:42, 17 June 2016
- Reference ?Paper XREF Movie Reference ?Paper XREF Movie7 KB (881 words) - 15:46, 21 November 2013
- ...No manual GO annotation from 26635 || || Role of met-1 not clear from this paper, but as a histone methyltransferase probably related to gene expression; ma ...made in close association between Gary and me, so the annotations for that paper should be kept.5 KB (825 words) - 21:25, 24 June 2013
- ...s/templates of suggested data/types that authors could/should submit for a paper *Curators cannot indicate both positive and negative for a data type per paper; conflict must be resolved by curators7 KB (1,123 words) - 16:39, 6 December 2012
- === Parasite Paper Pipeline and Curation Status Tracking ===4 KB (646 words) - 17:33, 1 September 2016
- Find (list) variations with a given phenotype, show phenotype, variation, and paper (query needs help) Find a paper based on a title:10 KB (1,650 words) - 18:12, 29 January 2024
- * Could some data (like paper class/data) go to the Alliance directly from Caltech? Could be quicker and * WB paper data would be ahead of the ACEDB paper data5 KB (777 words) - 13:18, 1 April 2021
- Reference ?Paper XREF Rearrangement3 KB (265 words) - 08:51, 5 October 2010
- Reference ?Paper XREF Describes_analysis ...erson XREF Describes_analysis // not always the same as the author of the paper - eg Erich running OrthoMCL8 KB (885 words) - 16:47, 21 December 2011
- **Evidence from more than one paper may be used within a single model **Evidence from more than one paper may be used to support a single assertion7 KB (1,004 words) - 17:50, 13 February 2017
- When papers are added to postgres using the Enter New Papers function of the Paper Editor, the corresponding abstracts are scanned, via a script, for matches ...people writing gene names this way. Could we make a rule that said if the paper is associated with GPR-1, then also automatically associate it with GPR-2?12 KB (1,973 words) - 20:53, 16 June 2011
- Reference ?Paper XREF Transgene Reference ?Paper XREF Transgene13 KB (1,341 words) - 20:12, 22 September 2015
- Reference ?Paper XREF WBProcess3 KB (275 words) - 01:07, 6 February 2014
- * simplified paper page -910 bytes (120 words) - 21:53, 19 January 2011
- Paper ?Paper XREF Interaction Paper ?Paper XREF Interaction12 KB (1,431 words) - 19:06, 20 March 2012
- modENCODE integrative paper submitted to Science!1 KB (134 words) - 19:02, 8 September 2010
- Back to [[Paper Pipeline]] =List of Paper Tables in Postgres (Alphabetical)=25 KB (3,238 words) - 16:42, 8 November 2019
- * Elsevier paper linking to WormBase, fixed search bugs so linking works correctly1 KB (164 words) - 16:51, 6 February 2015
- ...ng and organization of paper curation prioritization, curation is paper-by-paper, author response form is minimal - no specific author comments captured, ju5 KB (831 words) - 16:49, 1 December 2016
- * How many MODs curate paper-by-paper (for all datatypes at once) vs. our method, by datatype? ** WB & MGI curate by datatype, most others by paper (for all datatypes)9 KB (1,336 words) - 15:32, 2 June 2016
- ====Paper Acquisition==== ...opsis site on 10/28/2010 gives 55814 matches in 1421 documents, with total paper scores ranging from 660 to 7.14 KB (2,091 words) - 16:28, 9 December 2010
- ...pers]] or make mention of WormBase in the Acknowledgements section of your paper.2 KB (304 words) - 21:19, 5 July 2011
- WORM paper *We want a paper on the new website to go to a broader audience6 KB (903 words) - 16:37, 5 January 2012
- ===== Manually validate paper - topic flags without curating ===== ===== View all topic and entity flags for a given paper and validate, if needed =====9 KB (1,375 words) - 16:04, 18 April 2024
- **Start with curation of one paper together? ***Possible paper: [https://www.ncbi.nlm.nih.gov/pubmed/27881675 The Intestinal Copper Expor9 KB (1,377 words) - 16:44, 2 February 2017
- *For example, the Lehner et al., 2006 paper (WBPaper00027756) has a large number of RNAi experiments, but these are all ...se annotations where we don't already have the combination of a gene and a paper and a P annotation. I don't think we can include GO term in this diff, sin7 KB (1,164 words) - 17:54, 19 February 2015
- #Phenotype_info Paper_evidence ?Paper5 KB (352 words) - 17:20, 25 September 2015
- Paper : WBPaper00000005 There's an object that has no name and no type, but still has a paper.5 KB (749 words) - 19:47, 17 May 2018
- We are working with the authors of this paper: http://www.wormbase.org/db/misc/paper?name=WBPaper00028915;class=Paper8 KB (938 words) - 10:54, 21 December 2011
- Reference ?Paper XREF Picture3 KB (320 words) - 10:55, 10 December 2010
- ...pper right-hand corner of the screen with additional information about the paper including title, journal, year, and authors list: ...ith your name, e-mail address (if already provided), and PubMed ID of that paper pre-populated into the appopriate fields of the form:15 KB (2,325 words) - 23:32, 21 December 2015
- *** Add Paper and Public_name fields to the Features in the Nameserver? ** Prepare a paper list from each person23 KB (3,248 words) - 12:58, 22 September 2014
- * Putting together paper for AFP * Reviewing all user input for paper6 KB (897 words) - 14:27, 3 October 2019
- Also, once PMID is entered, form pulls up Paper information, meaning title etc etc, similar to what P2GO does; Kimberly wil 7. ''Enter the PMID of a published paper reference.''12 KB (1,838 words) - 18:16, 19 May 2015
- ...l has improved phrase search and combined supplemental documents with main paper documents; should roll out soon === Author First Pass paper ===7 KB (989 words) - 16:08, 5 February 2020
- * Raymond working on display for paper * Working on paper7 KB (1,010 words) - 17:08, 4 May 2017
- Reference ?Paper XREF Expr_pattern Reference ?Paper XREF Expr_pattern16 KB (1,695 words) - 08:29, 12 May 2014
- ...t UNIQUE #Evidence //source data, <WSversion> ?Sequence pos1 pos2 Evidence(Paper/person etc. remarks) Reference ?Paper XREF Allele8 KB (853 words) - 23:50, 16 April 2014
- | Array reference of Paper objects drawn from the Reference tag of an object. Got it?2 KB (271 words) - 14:09, 19 June 2014
- *Proposed modification to ?Paper and ?Person models to change 'Author_first_pass' -> 'ACKnowledge' (part of2 KB (261 words) - 00:39, 3 June 2022
- ** Such ?Genotype objects could be used repeatedly throughout a paper when applicable, but would likely not be used in any other papers (we would *Goal is to flag all data types in a paper and either curate at WB or share with a group that does curate that data12 KB (1,930 words) - 17:12, 1 February 2018
- ...Igor'') of the chapter name, URL, author(s), and DOI information for a new paper object to be added to WormBase.3 KB (508 words) - 15:41, 24 September 2007
- * Question about centralized paper repository; group needs guidance from Alliance PIs on how to proceed * Raymond working on writing paper4 KB (605 words) - 15:21, 3 March 2020
- === Paper author name === * Issue for WBPaper00048704: https://wormbase.org/resources/paper/WBPaper00048704#0--108 KB (1,189 words) - 14:10, 5 July 2018
- * We should point out response rate and paper coverage for community curation * Automated paper flagging and data identification (Karen)4 KB (640 words) - 19:07, 11 February 2016
- * wrong paper associations [https://github.com/WormBase/website/issues/1049 1049] -AC3 KB (412 words) - 18:10, 23 July 2013
- ...Curator, Community Curator Email, Unregistered Variation, and Unregistered Paper * Whenever an unregistered paper is entered Kimberly will be e-mailed8 KB (1,305 words) - 23:24, 3 June 2015
- ...use_package.pl<br>sym link: /home/acedb/xiaodong/antibody/use_package.pl ||Paper<br>Gene<br>Laboratory<br> || ||Xiaodong Wang|| ...e.pl<br>sym link: /home/acedb/draciti/oa_expr_ace_dumper/use_package.pl ||Paper<br> Gene<br> Anatomy<br> GO<br> Lifestage<br> Type<br> Transgene<br> Antibo20 KB (3,050 words) - 21:01, 19 April 2017
- Kimberly : Author just as Paper or also Person evidence ? Kimberly : Yes, if there is no paper.15 KB (2,374 words) - 16:00, 17 July 2014
- ...ome sequence, or data classes, and how they related to each other Alliance paper fig 2.2 KB (326 words) - 16:00, 8 September 2022
- *Where are relevant paper sentences stored? ''on tazendra /home/postgres/work/pgpopulation/genegenein Outline for NAR paper in the works7 KB (1,117 words) - 16:39, 4 August 2011
- | [[WormBase Model:Paper|Paper]] | http://beta.wormbase.org/reports/paper/WBPaper0001539212 KB (1,559 words) - 18:14, 15 June 2011
- WORM Paper Paper pipeline7 KB (1,064 words) - 19:12, 3 November 2011
- * We will begin annotating paper/review pathway images (with permissions) to WB topics ...s scan through papers from a new topic for relevance, they can also flag a paper for good diagrams4 KB (633 words) - 19:09, 6 January 2015
- ** Edit by Mary Ann - Paper submission deadline 15th Nov, 2014, Abstract submission deadline 1st Feb, 2 === Paper prioritization ===7 KB (1,079 words) - 19:04, 6 November 2014
- **paper (Kimberly - responded) ...ps://github.com/WormBase/website/issues/5743 Hello, I'm trying to access a paper c...]7 KB (1,077 words) - 16:26, 20 July 2017
- === NAR Paper === * Raymond working on methods paper for SObA display10 KB (1,586 words) - 15:30, 2 November 2017
- Reference ?Paper XREF GO_annotation3 KB (337 words) - 16:15, 19 February 2015
- Reference ?Paper XREF Transcript // [020306 kj]4 KB (350 words) - 09:32, 17 June 2013
- **Paper and curation pipeline *False negatives are automatically annotated as such when an SVM-negative paper is curated for the respective data type in the OA12 KB (1,878 words) - 15:55, 6 September 2012
- * Paper sent around to summarize Reactome model and curation pipeline * Can we have some automated/semi-automated way to update person evidence to paper evidence?6 KB (801 words) - 17:29, 2 July 2014
- Can we start collecting links to the online version of a paper, for easy access in the OA term info? ..., unfortunately, it is not obvious that supplemental materials exist for a paper that needs to be retrieved during PDF download, or where to get it example4 KB (622 words) - 16:47, 6 August 2014
- * Assigned manually from paper/reviews *Paper -- prt_paper -- '''Reference''' -- multi-ontology autocomplete on WBPaperID20 KB (3,088 words) - 19:17, 13 August 2020
- * Paper triage working group: It will be good if MODs can share their paper sources. Karen, Michael Mueller, and Kimberly will be involved in this WG.4 KB (694 words) - 21:33, 19 December 2019
- * Variation (nearly done) and Paper (25%) (TH)2 KB (271 words) - 16:42, 19 May 2010
- ...ms in GENETICS papers; this was brought up by Marek when he noticed that a paper could have benefited from protein complexes being linked to SGD GO pages.2 KB (361 words) - 23:31, 11 January 2011
- * Would be good to write a paper on automated concise descriptions ** Cannot search by section of paper9 KB (1,368 words) - 15:27, 4 October 2018
- === Paper ID converter tool === * The 'primary'/'nonprimary' paper status is updated automatically every night by a cron job7 KB (1,058 words) - 15:32, 2 April 2015
- Reference ?Paper XREF Anatomy_term5 KB (484 words) - 10:42, 10 August 2010
- ...pper right-hand corner of the screen with additional information about the paper including title, journal, year, and last name of the first author: ...ith your name, e-mail address (if already provided), and PubMed ID of that paper pre-populated into the appopriate fields of the form:26 KB (4,016 words) - 21:32, 8 April 2020
- * Adding tags to ?Paper and ?Person to track community curation more explicitly in WormBase2 KB (347 words) - 17:44, 7 November 2019
- **Molecule model - add Paper XREF2 KB (303 words) - 09:13, 5 October 2012
- ==Links by GSA Paper ID== | align="center" style="background:#f0f0f0;"|'''GSA Paper ID'''29 KB (4,227 words) - 18:16, 21 September 2011
- * Okay to cite WormBase, but also ask user to cite the WormBase paper (for now NAR, but in the future, Genetics)2 KB (325 words) - 15:24, 7 October 2021
- ** GO_term (addition to ?Paper)2 KB (296 words) - 01:51, 5 September 2015
- ...table describes the characteristics of each microarray dataset, including paper reference information, number and names of microarray conditions ... etc. The main algorithm of the SPELL search engine is described in the paper: Hibbs MA, et al. Exploring the functional landscape of gene expression: Di6 KB (964 words) - 18:49, 22 May 2018
- ...at specifications]. This allows us to map all gene products mentions in a paper to a MOD identifier and to a UniProtKB identifier so we can send annotation **Paper11 KB (1,765 words) - 15:10, 18 February 2014
- ...which papers to do, for example if the paper also has expression data, the paper can be curated at the same time for sequence features.5 KB (763 words) - 00:51, 19 September 2014
- Reference ?Paper ...ct will be created for every Strain-Strain (Host-Pathogen) interaction per paper that the interaction appears in, correct?15 KB (1,892 words) - 19:54, 10 February 2017
- Isolation Original_publication UNIQUE ?Paper Reference ?Paper XREF Antibody21 KB (2,888 words) - 19:58, 9 April 2021
- Reference ?Paper XREF CDS // added [011030 krb]4 KB (410 words) - 17:08, 17 August 2010
- ?Paper<br> Reference //paper where cluster was determined, for WS24215 KB (1,645 words) - 18:54, 23 January 2014
- ** Paper (XQ)2 KB (280 words) - 19:14, 10 August 2010
- 2. On the next page, you'll be presented with a box for entering paper IDs and two options for action: Load Sentence File3 KB (408 words) - 23:34, 13 August 2010
- The link to Wormbase will point to the paper page showing the referenced curated data e.g. http://www.wormbase.org/resources/paper/WBPaper00001770#30--103 KB (427 words) - 18:31, 3 October 2013
- === NAR Paper === * Todd wants to describe new WormBase approach in a different paper8 KB (1,225 words) - 16:33, 3 October 2013
- * Currently, Textpresso searches in paper main documents and all individual supplemental documents separately ...to search on a single, consolidated file containing the main document of a paper AND the supplementals?5 KB (747 words) - 16:31, 5 December 2019
- * Considering SVM for disease; current paper flagging pipeline is rather broad * Results section are not being extracted in latest Textpresso (paper sectioning in general not happening)9 KB (1,364 words) - 15:39, 7 February 2019
- ?Paper3 KB (475 words) - 14:53, 19 February 2013
- *The input is a list of paper IDs for known positive papers for a given data type.3 KB (425 words) - 22:35, 16 August 2010
- ** Paper-gene connections; Kimberly responded; can we close?3 KB (415 words) - 15:31, 24 December 2018
- *Searches can also be performed using gene names, paper IDs, component terms in sentences, and GO terms - searches could be perform **What is unique about an annotation? - File, Paper, Sentence, Gene product, GO term, GO evidence code, Curator, Date30 KB (4,868 words) - 14:50, 11 June 2013
- *How many objects per paper (average, distribution?)? *Curation stats per paper (Raymond): write comments in a remark field; traceable, transparent, availa5 KB (843 words) - 17:26, 1 November 2012
- * WormBase Genetics paper reviewer's feedback3 KB (432 words) - 17:19, 18 January 2024
- * Chris working with Textpresso to identify ontology terms from paper text for suggestion to community annotators ** We will require: Author name, author e-mail, paper/publication ID, sequence info (sequence, PCR_Product, Ahringer well locatio5 KB (843 words) - 16:32, 4 December 2014
- ...ence UNIQUE ?Paper XREF RNAi //[070215 ar2] made reference unique so Paper sort of #Phenotype_info Paper_evidence ?Paper29 KB (4,152 words) - 20:29, 30 July 2019
- Propose to submit paper on Community Curation === Handling retracted paper ===8 KB (1,220 words) - 16:26, 3 September 2015
- === Elsevier paper-linking through Scholix === ...ld be good to revisit the paper page display for what is referenced in the paper11 KB (1,703 words) - 15:27, 5 April 2018
- ...:GFP, in this case, the transgene is mgIs18, but not stated as such in the paper. The expression “[ttx-3::GFP]” in the Summary of mgIs18 in acedb3 KB (415 words) - 21:29, 23 July 2013
- ! [http://dev.wormbase.org/db/misc/paper?name=WBPaper00031858;class=Paper 00031858] ! [http://dev.wormbase.org/db/misc/paper?name=WBPaper00035152;class=Paper 00035152]3 KB (521 words) - 18:57, 10 August 2010
- === Alliance Literature Paper Tags === ...f data provenance from the Hobert’s lab. Unless Oliver published this in a paper that was eluded from our flagging system (e.g. flagged SVM negative).9 KB (1,377 words) - 16:36, 4 March 2021
- ==WormBase - manual annotation, multiple annotations from a single paper (also includes an entry in the With/From column)== ==Phenotype2GO Pipeline - RNAi Phenotype2GO (Notes: Would like to have both a Paper reference and a GO_REF that describes the methodology for Phenotype2GO Mapp17 KB (2,104 words) - 22:44, 17 December 2014
- ** October 31, 2019 - Paper Submission Deadline * Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group);13 KB (2,025 words) - 16:28, 7 November 2019
- * Kimberly and Juancarlos could deal with Paper-based problems.3 KB (440 words) - 08:42, 3 September 2020
- ...'categories''' and '''keywords''' to identify sentences in the text of the paper. 3. ‘Materials and Methods’ section of paper15 KB (2,102 words) - 05:17, 25 September 2014
- ** look for potential reviewers of a paper based on similar text content * Could we retroactively deal with paper-gene connections? We could possibly look in Postgres history tables to see11 KB (1,782 words) - 17:55, 13 May 2021
- * Paper-by-paper approach vs. big-picture approach ...d to be micropublication-specific differences, e.g. don't need to submit a paper ID8 KB (1,229 words) - 15:31, 1 June 2017
- ====Paper Acquisition==== =====Filtering by Paper Section=====24 KB (3,814 words) - 18:31, 8 August 2011
- ...ert : some published alleles are falling through the cracks for curation; paper mentioned is missing sequence and phenotype3 KB (436 words) - 15:07, 22 July 2019
- *NAR paper status - due the 15th, was it sent off?3 KB (420 words) - 16:02, 17 August 2017
- ** Do we want to display these published diagrams on ?Paper pages and/or ?Topic pages ...bout some specific curated datatypes to a file we already supply that maps paper and gene identifiers6 KB (974 words) - 17:28, 3 September 2014
- ** Postgres in cloud; forms local? Paper pipeline? ...posed to using a file for neuronal term groupings taken from Oliver Hobert paper in the old pipeline)9 KB (1,366 words) - 15:19, 6 September 2018
- *Fabric printing comparable in cost to paper3 KB (436 words) - 17:59, 11 July 2013
- Reference ?Paper XREF Clone Reference ?Paper XREF Clone10 KB (1,176 words) - 22:24, 18 March 2014
- ** So far we've received one, accidental, flagging of a paper for allele-phenotype data; one submission by Paul3 KB (425 words) - 13:54, 8 July 2015
- * Kimberly's Species tag in Paper model will be added for WS2344 KB (503 words) - 08:30, 22 June 2012
- *If a region is asserted to be a promoter region in the paper and it is within 200bp (or thereabouts?) of the 5' of the target gene and i ...ple 2 from WBPaper00003631 (hypothetical made up example- in this specific paper there's not such evidence but might be a scenario):'''24 KB (3,538 words) - 17:50, 15 December 2015
- [[Sample paper and data for exploring updates]]2 KB (306 words) - 15:01, 14 January 2016
- *Develop paper-viewer? Apart from CAT, text mining flow? Separate module *Keep an eye out for PDF(paper) viewers/editors/annotators7 KB (1,019 words) - 20:58, 12 April 2012
- Paper pipeline *Subtract papers that are already curated from the paper pool9 KB (1,302 words) - 16:38, 2 June 2011
- * Bob Goldstein's group prepared software tools in their paper; could we make use of them? ...ll be made if a second paper uses the same disease model (described in the paper being curated) and adds a treatment to it to show amelioration or exacerbat9 KB (1,490 words) - 15:35, 6 October 2016
- * Can we create Paper objects for the actual emails or other forms of communication (figure out d * How much will it muddy things to create Paper objects for emails, e.g. how will it affect NLP downstream, do we need PDFs10 KB (1,547 words) - 21:31, 2 January 2024
- ...s will record dead papers from pap_status and dead genes from gin_dead<br> paper term info will show cns_name, cns_publicname, cns_constructionsummary, cns_ |Reference||cns_paper||Multiontology||Paper||||all||WBPaper||pap_tables||-||one-time copy from trp_paper||37 KB (5,333 words) - 19:07, 27 June 2019
- ...terested in displaying the single cell embryo data from their 2019 Science paper in WormBase3 KB (563 words) - 03:27, 19 March 2022
- Paper published by NCSU:3 KB (462 words) - 16:11, 15 December 2011
- **paper starts at WBPaper00028425, ends at WBPaper00035225 Paper ?Paper XREF Interaction50 KB (5,228 words) - 15:10, 21 July 2017
- *Easy to add the genotype information when a curator is reading the paper, and to do it at the same time as request for the ID3 KB (523 words) - 11:20, 3 April 2020
- *Maybe we will name according to paper e.g. "WBPaper########_Ex####" ...g after WBPaper was giving problems (i.e. dealing with 430 objects with no Paper attached and other minor issues).7 KB (1,070 words) - 17:47, 1 March 2012
- * Each paper has their own pipelines/processes for analysis of data; how do we want to c3 KB (501 words) - 17:29, 1 September 2016
- ...sion number' field in the OA, and dumps that entry, if empty, looks at the Paper field and dumps that.4 KB (629 words) - 18:27, 23 November 2020
- ...ve a user who is requesting help in naming this locus in C. briggsae for a paper. Ron can of course use the nurf-1.c and nurf-1.e nomenclature in his paper for marking up his transcripts/Isoforms and having a clear naming conventio8 KB (1,391 words) - 11:57, 6 August 2014
- Reference ?Paper XREF Gene #Evidence7 KB (712 words) - 10:40, 4 October 2010
- ...making it impossible to tell which remark (e.g. "Table 3") goes with which paper8 KB (1,213 words) - 15:29, 6 July 2017
- *Pub field -> paper.obo Variation-gene, variation-paper connections are used to select for variations of type allele or those that10 KB (1,644 words) - 18:48, 13 August 2020
- **What paper sets (e.g. all papers going forward vs older papers)?4 KB (641 words) - 15:23, 19 June 2012
- ...ipt that Cecilia also runs manually based on other verified authors in the paper sharing a Lineage or Laboratory *Prioritize name and e-mail verification for new paper/person connections?7 KB (1,103 words) - 18:28, 5 May 2011
- * Chris - UniProt wants additional information on genes from paper classification.4 KB (645 words) - 08:57, 27 August 2014
- ...ake a genome-wide graphic like the original 1998 C. elegans genome project paper https://github.com/WormBase/website/issues/82744 KB (576 words) - 16:28, 17 June 2021
- ***Numbers by object # versus paper # **Curation by paper, data type, topic/process?10 KB (1,553 words) - 18:04, 7 February 2013
- * Juancarlos - Build API for paper, person, lab ? * Stavros - Apollo can track paper-gene connections, could expand to handle persons and other stuff.9 KB (1,570 words) - 16:36, 21 September 2023
- ...ase.org/wiki/index.php/New_Paper_Model_-_Model_and_Changes_to_Pipeline New Paper Model] 00000351 could remove In_book paper, since this is a Monograph - stands on its own. LINK OUT to BHL!15 KB (1,605 words) - 23:38, 13 August 2010
- ...(2001), PNAS 98, 218-223] (SMD data from Kim laboratory's 2001 microarray paper)5 KB (646 words) - 17:11, 25 November 2020
- Reference ?Paper XREF Transgene "...paper.sup.1" means the transgene name was mentioned in the supplementary file.29 KB (4,575 words) - 16:23, 3 March 2022
- *Paper -- gop_paper4 KB (759 words) - 23:35, 26 February 2017
- * There are problems; paper IDs keep switching columns ...ely pre-publication); we will likely point to a consortium as source until paper is published8 KB (1,121 words) - 14:01, 15 July 2019
- |||Gene Symbol (main/other/sequence) '''Genes studied in this paper''' [http://tazendra.caltech.edu/~postgres/cgi-bin/curation_status.cgi?actio ...ene expression in genetic background if mentioned in paper. '''Basically, paper reports changes or lack of changes in gene expression level or pattern due21 KB (3,156 words) - 23:03, 13 August 2010
- * Paper PDFs stored on /home2 as the primary storage location * WB data is paper-centric, unlike data in modSeek8 KB (1,147 words) - 15:33, 7 May 2015
- ...from the sentence saver, this will display all the textpresso results by paper. <br>4 KB (704 words) - 18:19, 28 June 2011
- ! Figure in Paper |New GO term requested for this paper.16 KB (1,999 words) - 18:24, 28 October 2015
- | :paper/directory | ?Paper35 KB (4,174 words) - 10:52, 2 February 2015
- model? It seems pretty redundant with the Paper information and I'm not4 KB (599 words) - 00:25, 4 May 2012
- **WSExpr_pattern.ace - used to make paper-data type connections for UniProt **WSGO_annotation.ace - used to make paper-data type connections for UniProt18 KB (2,743 words) - 17:14, 16 March 2023
- ** RT - Sanger worm-bug@sanger.ac.uk - Poss retirement? Effect Caltech paper submissions for Hinxton/UK curators4 KB (708 words) - 16:41, 16 July 2015
- **This file maps PubMed identifiers to MOD paper IDs. A script will run with ccc scripts every time to generate this univer '''5)''' Link out paper IDs in the display to PubMed or MOD11 KB (1,666 words) - 17:53, 19 June 2014
- | [[WormBase Model:Paper|Paper]] | Target for removal - Unused data class, appears to have been replaced by paper (need to check acedb dependencies)16 KB (2,207 words) - 23:06, 9 January 2014
- These stages are defined in the paper [http://www.sciencemag.org/cgi/content/full/326/5950/236#R2 "Genome Project5 KB (723 words) - 09:02, 22 May 2012
- *** Example paper: WBPaper00046571 - afp flagged for geneint and newmutant in curation status ==== OA Paper Ontology switching to ABC ====36 KB (4,994 words) - 17:27, 14 February 2024
- * Paper editor may be best form to start Datomic transition, since it doesn't deal4 KB (571 words) - 16:48, 3 March 2016
- ...oliters (0.006 cubic millimeters) [see Table 2, Figure 1A, and Figure 3 of paper]. Another good reference for larval size is (Knight C. et al (2002) Evol De12 KB (1,699 words) - 18:02, 13 July 2012
- ...ntary data section of the "Integrative analysis of Functional Elements..." paper. ...xgap-minrun" algorithm instead of the "MSTAD" program, as described in the paper.17 KB (2,478 words) - 14:07, 5 July 2012
- * Michael will send around paper list with new and old results in the same file ** Analogous to FlyBase's 'Fast Track Your Paper' (FTYP)11 KB (1,676 words) - 15:28, 2 May 2019
- ...three action buttons on the top - Submit, Search for Sentence, Search for Paper | align="center" style="background:#f0f0f0;"|Paper ID17 KB (2,749 words) - 20:04, 21 January 2011
- NAR 2011 Paper working draft4 KB (650 words) - 17:08, 1 September 2011
- ...nue. NBP alleles are handled a bit differently and do not need a person or paper reference to be saved.5 KB (782 words) - 20:35, 24 September 2010
- * Waterston paper ...concerned about the reported/assumed/inferred identity of the cells in the paper12 KB (1,809 words) - 16:33, 1 March 2018
- ** WormBase curates to datatypes, most other MODs curate all data per paper.4 KB (743 words) - 12:22, 5 March 2021
- * Is this adaptable for the other MODs/organisms? Will submit the paper first4 KB (604 words) - 15:28, 5 May 2016
- ...experiments for the WITH column. Or, if making an IGI annotation for the paper, have a drop down list of all genes mentioned in the paepr. Similarly, whe ...ect where cursor is placed in the editor window, e.g. Paper should reflect paper info20 KB (3,124 words) - 19:59, 19 February 2020
- * PubMedID -submissions are novel data, do not have a paper attached. Submissions will get their own WBPaperID5 KB (800 words) - 18:29, 16 August 2017
- analysis paper describing the five currently sequenced Caenorhabditis genomes.6 KB (661 words) - 16:51, 21 December 2011
- ...o view curation status results for (see below). This page includes a Topic paper filter to search for papers related to a WormBase Biological Topic. == Specific Paper Page ==144 KB (18,174 words) - 19:56, 21 January 2021
- Duplicon region features from paper WBPaper00034747 http://www.wormbase.org/db/misc/paper?name=WBPaper00034747;class=Paper6 KB (675 words) - 16:42, 21 December 2011
- ...st way to fix these seems to be to check the annotations to the associated paper in Protein2GO (by entering the PMID into the search box) and then update th ...genes to paper connection for Daniel Shaye, these genes were added to the paper editor, so this file is no longer manually being put into citace.23 KB (3,744 words) - 15:12, 23 December 2022
- **One caveat: if author's potentially correct data in the paper when they submit the strain data to the CGC, how would we reconcile that?5 KB (816 words) - 16:43, 17 May 2018
- * Ranjana et al working on paper ...rators (Xiaodong, Daniela, etc.) to create and approve the ?Features for a paper10 KB (1,485 words) - 18:08, 5 March 2014
- *Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" version of ACe4 KB (695 words) - 14:44, 3 December 2020
- **Original report from paper by Chris Li et al4 KB (651 words) - 16:11, 2 May 2013
- * Paper corpora for all species [MM & MZ]5 KB (787 words) - 18:10, 25 August 2022
- Paper ?Paper XREF Interaction 'Paper' = int_paper53 KB (6,521 words) - 20:51, 7 March 2019
- *mass spec [[(1 paper)]]5 KB (746 words) - 18:57, 10 August 2010
- Reference ?Paper Reference ?Paper XREF Transgene20 KB (2,339 words) - 18:04, 23 September 2015
- ...s (especially for WormMine) on the website, and possibly including one for paper curations. Consider placing links to these videos on the relevant page in a - Provide a table for authors to fill before submitting a paper (example - flybase https://wiki.flybase.org/wiki/FlyBase:Author_Reagent_Tab11 KB (1,649 words) - 16:10, 19 July 2018
- ...it's not on the seq browser. Magda can help but she will need to study the paper6 KB (982 words) - 16:54, 1 September 2022
- Reference ?Paper XREF Life_stage ...add A UNIQUE ans #Evidence hash in the Definition, in order to capture the paper evidence.14 KB (2,213 words) - 19:26, 12 February 2019
- * Curate paper-by-paper * Not clear if it needs to be a full paper; can we resubmit Biocuration meeting abstract?14 KB (2,226 words) - 15:31, 7 June 2018
- ...these data are being provided in advance of publication of the five-genome paper (coordinated by Erich Schwartz).6 KB (764 words) - 16:45, 21 December 2011
- * Kimberly will send out the AFP form for the paper when5 KB (670 words) - 15:31, 3 June 2021
- #'''Reference (dis_paperexpmod)''': Autocomplete drop-down with WB Paper list ...nly if used in a single experiment to model a single disease from a single paper, they should all be consistant with the modifier_association_type chosen36 KB (4,595 words) - 18:10, 15 March 2023
- *Paper stats vs. data type stats5 KB (752 words) - 17:07, 7 July 2011
- This page requests information about the paper (e.g. WBPaperID), laboratory two-letter code (usually senior/corresponding ...erate an *.ace file, select "No" next to "Add another experiment from this paper?". Finally, indicate whether or not you would like to receive an e-mail of47 KB (7,989 words) - 23:40, 1 September 2015
- !Use - Paper or meeting abstract gene connection8 KB (1,375 words) - 05:12, 21 April 2020
- ** SVM paper => gene curation5 KB (741 words) - 10:57, 21 August 2015
- ** Yet another C. elegans reference sequence error paper (Zhang). ** RT-sanger worm-bug@sanger.ac.uk >1000 of paper tickets11 KB (1,714 words) - 11:04, 27 July 2015
- ** This results in (1) column 6 having a mix of paper/reference IDs (good) and WBVar IDs (not good) and (2) WBVar IDs split betwe6 KB (861 words) - 19:23, 5 November 2020
- ...sers can still trace back to which genotype the authors referred to in the paper originally6 KB (911 words) - 17:13, 6 June 2019
- *WikiPathway curation would be best while curating a paper; update on WikiPathways site for other curators to see ...curating a data type, there are many more aspects of the biology from the paper that inform the curator of the pathway13 KB (1,983 words) - 16:40, 7 November 2013
- *We will try to generate an ACEDB patch every other month, starting with the Paper class data *Paper .ACE file: Would include bibliographic info, journals, authors, genes assoc13 KB (2,097 words) - 22:48, 7 April 2011
- | Finish up annotations for other genes in the paper11 KB (1,225 words) - 19:03, 19 March 2018
- ...tics/for_authors/general.html Bioinformatics] - Proposed <i>conference</i> paper/Letter to Editor ...fordjournals.org/nar/for_authors/criteria_scope.html NAR] - Survey/Summary paper21 KB (3,246 words) - 23:20, 13 August 2010
- * New species are associated with paper objects, but otherwise no additional data for those species come from Calte5 KB (880 words) - 15:40, 3 September 2020
- | align="center" style="background:#f0f0f0;"|'''Paper Flagging Methods (triage)'''9 KB (1,174 words) - 18:30, 29 August 2012
- ...ease add a button link to Person-editor to possible two. When curating new paper to mark possible match as real possible two, Example WBPaper00039714, 13141 '''WBPaper00039713 none of the Person's linked to this paper were sent emails for verification june 28, 2011. This is 1 example only'''119 KB (18,888 words) - 00:05, 2 May 2014
- *paper(column 6) ...line and use only one variation, with same phenotype, NOT(if exists), and paper as original line<br>36 KB (5,076 words) - 01:38, 2 March 2016
- *What about paper objects then?6 KB (944 words) - 16:25, 1 November 2012
- Gen. nematoda phylogeny paper7 KB (1,220 words) - 15:50, 25 November 2011
- *1541 - Multiword string search Paper class - Michael P., Xiaodong, Karen, Kimberly, Abby6 KB (1,069 words) - 20:52, 23 July 2013
- *[[Phenotype2GO Paper Inclusion List]] **Reference: if a published paper is used as evidence.30 KB (3,904 words) - 18:45, 13 May 2020
- ...e first time including gene predictions imported from Ralf Sommer's group (paper in press). We have8 KB (936 words) - 16:48, 21 December 2011
- ...e good to ask authors if they had to omit data from the recently published paper and if they want to micropublish6 KB (921 words) - 16:52, 4 January 2018
- ** Talk 4: Be ACKnowledged and help us curate your paper! (10 mins + 5 mins for questions)7 KB (1,113 words) - 18:19, 6 April 2023
- Reference ?Paper XREF Sequence12 KB (1,258 words) - 09:29, 5 October 2010
- Paper ?Paper XREF Interaction Paper ?Paper XREF Interaction59 KB (8,367 words) - 22:00, 14 December 2018
- !Use - Paper or meeting abstract gene connection9 KB (1,464 words) - 14:10, 29 May 2015
- * '''Pub''' - app_paper - ?Paper (Ontology) * '''Unregistered Paper''' - app_unregpaper - NOT DUMPED - Text (Text)23 KB (3,334 words) - 19:01, 31 October 2017
- * ?Movie linking - Added Reference ?Paper XREF Movie and DB_INFO tags8 KB (1,246 words) - 15:52, 12 November 2013
- Third, if you have a paper about to come out, feel free to send us a pre-print and we can get a head s7 KB (1,180 words) - 11:00, 21 December 2011
- ...booth? Shall we have an extra poster instead? The banner could be a cheap paper one8 KB (1,231 words) - 22:06, 25 July 2017
- *authors do not curate their whole paper7 KB (1,249 words) - 17:23, 7 January 2016
- ...re dumping the papers file, double-check the 'Find Dead Genes' list on the paper editor and make any necessary updates. ...e description. The paper in parentheses after the gene name is the recent paper that prompted adding the gene to the list, but may not be the only relevant47 KB (6,852 words) - 04:27, 8 December 2020
- |cns_paper||Paper||one-time copy from trp_paper10 KB (1,537 words) - 17:05, 28 May 2021
- Reference ?Paper XREF Picture ...iology paper but the rules of handling the pictures are universal and not "paper specific".120 KB (19,719 words) - 16:44, 20 October 2023
- **Streamlining the paper acquisition/curation process7 KB (1,158 words) - 17:20, 3 May 2012
- but we have someone at Caltech that works on associating a paper's ...h.edu/~azurebrd/cgi-bin/forms/journal/journal_first_pass.cgi?action=Curate&paper=00000001&passwd=1241223658.141896714 KB (2,365 words) - 21:14, 23 July 2013
- -rwxrwxr-x 1 todd wormbase 11723 Jul 6 14:06 paper16 KB (1,576 words) - 17:44, 16 August 2010
- * Text, Paper viewer (SAB was excited about)8 KB (1,218 words) - 17:46, 2 April 2014
- ...notype curators could curate genetic AND physical interactions in the same paper8 KB (1,120 words) - 16:19, 5 March 2015
- Reference ?Paper XREF DO_term Paper_evidence UNIQUE ?Paper// Addition of 'UNIQUE' for WS26132 KB (3,649 words) - 20:55, 21 May 2020
- > Reference ?Paper XREF Clone < Reference ?Paper XREF Clone235 KB (23,325 words) - 10:33, 3 July 2014
- * Do we offer text fields for authors to indicate where the data is in the paper? May be asking too much and difficult to implement8 KB (1,262 words) - 15:34, 3 May 2018
- ...4dU4tSW43cFc2TE5wemc&usp=sharing Conservation Matrix] based on the Grishok paper and WS241 (3rd sheet).10 KB (1,194 words) - 16:35, 13 December 2013
- * Do we know how many labs are still viable? Check for a paper verified in the last 5 years, or requested strains from the CGC recently8 KB (1,228 words) - 20:57, 14 July 2020
- ** [https://pubmed.ncbi.nlm.nih.gov/2006412/ Bargmann (1991)] ablation paper; start at beginning9 KB (1,369 words) - 22:47, 5 August 2020
- *Do Paper Editor modifications (e.g. False Positive flagging) transfer to the Curatio9 KB (1,339 words) - 19:02, 31 January 2013
- ** Send out the MIMB paper to funders to give them an overview11 KB (1,898 words) - 16:43, 7 June 2018
- | 4213||sos-1, T28F12.3, St. Louis sequence, paper shows 17 exons. ||17:58.3 ...uence correction K08A8.1 St. Louis, see fig.2; Wormbase shows eight exons, paper shows five. ||48:45.740 KB (4,083 words) - 23:02, 13 August 2010
- Reference ?Paper XREF Expr_pattern *''Reference'' -- Reference "exp_paper" -- multiontology on paper WBPaperID - multiontology there are Expr objects with multiple papers as104 KB (15,303 words) - 19:39, 11 May 2023
- = Methods & Approaches for Paper Categorization =10 KB (1,279 words) - 18:20, 18 October 2013
- *Is there a way to update curators if a new paper is added to the current focus topic?10 KB (1,583 words) - 18:16, 5 February 2014
- Reference ?Paper XREF Molecule Reference ?Paper XREF Molecule50 KB (6,966 words) - 19:15, 13 August 2020
- * Cecilia can present on person curation (persons, paper-person connections)10 KB (1,527 words) - 15:32, 6 April 2017
- *put them in paper class? no10 KB (1,453 words) - 18:52, 4 February 2015
- ...ssociated with genes in either the 'results' section or the 'body' (if the paper can not be sectioned), then one would execute the following:15 KB (2,321 words) - 17:36, 18 August 2017
- ...n WBPaper pages to link out the the external databases affiliated with the paper, including a link to our FTP site with shared data files, maybe?10 KB (1,464 words) - 17:09, 13 August 2015
- *Order of the data will be: WBGene, Date, Paper, Accession_evidence, Automated_concise_description, Inferred_automatically14 KB (1,958 words) - 20:14, 2 January 2015
- Back to [[Paper Pipeline]]10 KB (1,402 words) - 17:53, 2 November 2010
- ***Format: "name/id(paper)" with evidence drop-down when clicked for all types - Alleles, Transgenes, ...nteraction objects affiliated with this interaction. I would expect to see paper references in a "Citations" column. Could we perhaps put the interactions u29 KB (4,254 words) - 20:25, 27 April 2012
- * Have to fill out request forms for (each?) paper that we request ...tion is <http://www.wormbase.org/tools/tree/run?name=WBPaper00024671;class=Paper;expand=Refers_to#Refers_to>, and the dataset is Expression cluster » WBPa11 KB (1,664 words) - 16:29, 7 December 2017
- The Lamm et al. (2011) paper describes three techniques for doing16 KB (1,820 words) - 14:15, 13 September 2012
- ?Paper17 KB (2,002 words) - 14:17, 13 September 2012
- They are from the paper:17 KB (1,988 words) - 11:15, 21 December 2011
- **Do not use data from lines with the Paper Reference: WBPaper00040986 **exp_paper for paper65 KB (9,380 words) - 22:39, 5 July 2018
- ...GO Transgene info: name : WBTransgene00000659 trp_publicname : Is34(eEx85) Paper : WBPaper00003958 trp_summary : [(mab-9::GFP + pCes1943)].||yes|| transgene21 KB (3,194 words) - 02:08, 17 May 2018
- published data vs unpublished data - paper not finished yet, or secretive reasons TCGA paper: pathway covers 60% of patients. Go to pathways commons - missed it.37 KB (5,533 words) - 19:17, 11 April 2014
- published data vs unpublished data - paper not finished yet, or secretive reasons TCGA paper: pathway covers 60% of patients. Go to pathways commons - missed it.37 KB (5,533 words) - 19:17, 11 April 2014
- Back to [[Paper Pipeline]]32 KB (4,339 words) - 17:40, 2 November 2010
- 2. decided by conferring with validator. Is that fact in the paper? Simple task. Decided in the end - curator would look at the fact. Detailed29 KB (4,082 words) - 19:15, 11 April 2014
- Paper - poster here #831 KB (4,384 words) - 19:08, 11 April 2014
- ...fp.</i> Such abbreviations should be clearly defined where first used in a paper.</p><p><li>An engineered insertion of GFP plus the <i>unc-119</i>(+) select56 KB (9,514 words) - 09:48, 23 October 2015
- ...fp.</i> Such abbreviations should be clearly defined where first used in a paper.</p><p><li>An engineered insertion of GFP plus the <i>unc-119</i>(+) select56 KB (9,520 words) - 11:51, 21 October 2015
