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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
