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Page title matches

  • Paper Pipeline
    #[[2010 - Paper Pipeline: Documentation and Instructions]] #[[New Paper Model - Model and Changes to Pipeline]]
    1 KB (130 words) - 21:21, 15 March 2021
  • Paper Type
    ...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 bet
    2 KB (259 words) - 18:08, 16 August 2010
  • (1 paper)
    ! [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
  • Paper Editor
    #REDIRECT [[Using the Paper Editor]]
    36 bytes (5 words) - 21:39, 8 May 2011
  • Gene-Paper Associations
    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 (Octobe
    1 KB (164 words) - 23:35, 14 February 2011
  • Using the Paper Editor
    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 make
    7 KB (1,204 words) - 18:58, 30 June 2014
  • WormBase Model:Paper
    // ?Paper class - krb 040223 // ?Paper class - krb 040223
    5 KB (471 words) - 16:07, 4 October 2010
  • Gene-Paper Connections
    Back to [[Paper Pipeline]]
    71 bytes (11 words) - 21:51, 11 May 2011
  • Genetics Paper Pipeline
    ...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
  • WormBase Paper Categorization
    = Methods & Approaches for Paper Categorization =
    10 KB (1,279 words) - 18:20, 18 October 2013
  • Paper editor.cgi code
    90 bytes (15 words) - 13:16, 5 November 2018
  • Paper Pipeline Scripts
    =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
  • Entering New Paper Objects
    =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
  • Phenotype2GO Paper Inclusion List
    [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 screen
    2 KB (313 words) - 18:20, 16 August 2010
  • Paper Tables in Postgres
    Back to [[Paper Pipeline]] =List of Paper Tables in Postgres (Alphabetical)=
    25 KB (3,238 words) - 16:42, 8 November 2019
  • Paper ID conversion CGI
    ...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
  • Paper Pipeline - To Do List
    '''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. -- DONE
    7 KB (1,103 words) - 18:08, 16 August 2010
  • UniProt Paper - Gene - Data Type
    * 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
  • 2010 - Paper Pipeline: Documentation and Instructions
    Back to [[Paper Pipeline]] =Paper Pipeline Documentation=
    412 bytes (47 words) - 15:19, 15 April 2011
  • Adding pmid Identifier to Paper Object
    '''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
  • Paper Pipeline To Do - May 2011
    #[[Gene-Paper Connections]] #[[Genetics Paper Pipeline]]
    388 bytes (49 words) - 20:02, 15 April 2011
  • Sample paper and data for exploring updates
    '''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
  • New Paper Model - Model and Changes to Pipeline
    Back to [[Paper Pipeline]] History Merged_into UNIQUE ?Paper XREF Acquires_merge
    10 KB (928 words) - 18:34, 2 May 2011

Page text matches

  • XML Status Tag
    ...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
  • Paper Pipeline
    #[[2010 - Paper Pipeline: Documentation and Instructions]] #[[New Paper Model - Model and Changes to Pipeline]]
    1 KB (130 words) - 21:21, 15 March 2021
  • Primary data Tag
    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
  • Paper Pipeline To Do - May 2011
    #[[Gene-Paper Connections]] #[[Genetics Paper Pipeline]]
    388 bytes (49 words) - 20:02, 15 April 2011
  • Adding Missing Authors
    '''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 a
    588 bytes (110 words) - 18:55, 3 March 2011
  • Missing Abstracts in PLoS One, PLoS Biol Papers
    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
  • 2010 - Paper Pipeline: Documentation and Instructions
    Back to [[Paper Pipeline]] =Paper Pipeline Documentation=
    412 bytes (47 words) - 15:19, 15 April 2011
  • Removing Dead Genes from Papers
    ...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
  • WS235 Models.wrm
    === Molecule class to paper class connectivity === Reference ?Paper XREF Molecule
    587 bytes (86 words) - 10:07, 28 November 2012
  • Handling Corrections and Errata
    ...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 pipelin
    1,004 bytes (161 words) - 20:09, 15 April 2011
  • Type - mapping of current to future Type
    '''Mapping of current ?Paper Type to new ?Paper Type:''' Note: all ?Paper Types are listed, even if there is no change to the text. However, new or
    1 KB (205 words) - 17:49, 17 August 2010
  • Gene-Paper Associations
    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 (Octobe
    1 KB (164 words) - 23:35, 14 February 2011
  • WBConfCall 2023.12.07-Agenda and Minutes
    === 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, para
    1 KB (159 words) - 18:22, 7 December 2023
  • Deleting Authors
    ...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
  • Books
    '''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 a
    372 bytes (60 words) - 20:54, 10 August 2010
  • Doodle Polls for conference call scheduling
    === Paper ===
    944 bytes (131 words) - 20:41, 13 August 2010
  • WS275 Models.wrm
    * Paper retraction
    134 bytes (16 words) - 11:57, 2 January 2020
  • Type
    '''Mapping of current ?Paper Type to new ?Paper Type:''' Note: all ?Paper Types are listed, even if there is no change to the text. However, new or
    1 KB (183 words) - 17:49, 17 August 2010
  • Paper ID conversion CGI
    ...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
  • WBConfCall 2023.02.02-Agenda and Minutes
    *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
  • Paper Type
    ...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 bet
    2 KB (259 words) - 18:08, 16 August 2010
  • First-pass to Curation
    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
  • Gene-Paper Connections
    Back to [[Paper Pipeline]]
    71 bytes (11 words) - 21:51, 11 May 2011
  • Adding Papers not in PubMed
    ...'' 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
  • Entering New Paper Objects
    =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
  • WormBase Model:SAGE experiment
    // connects to condition and paper objects Reference ?Paper XREF SAGE_experiment
    543 bytes (47 words) - 09:05, 5 October 2010
  • Overall performance
    ! 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
  • Understand the pipeline by looking at all scripts and forms
    ==Paper Tables== ==Paper Editor==
    4 KB (536 words) - 20:31, 25 April 2011
  • Meeting Abstracts
    **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
  • What to do about new gene names not yet in WB
    Back to [[Paper Pipeline]]
    93 bytes (14 words) - 13:33, 5 January 2010
  • Meeting abstracts
    Back to [[Entering New Paper Objects]]
    151 bytes (24 words) - 15:41, 8 April 2010
  • WormBase Model:Paper
    // ?Paper class - krb 040223 // ?Paper class - krb 040223
    5 KB (471 words) - 16:07, 4 October 2010
  • WormBase Model:Author
    Paper ?Paper
    715 bytes (81 words) - 11:06, 10 August 2010
  • Write up a summary of the weekly checking script - Kimberly and Juancarlos
    Takes postgres paper entries '''missing''' author, pages, title, type and year and checks PudMed
    169 bytes (25 words) - 10:51, 21 July 2009
  • What to do about non-standard nomenclature
    Back to [[Paper Pipeline]]
    169 bytes (27 words) - 15:13, 5 January 2010
  • WormBase Model:Person
    Publication Paper ?Paper XREF Person #Evidence Not_paper ?Paper XREF Not_person #Evidence
    3 KB (272 words) - 16:10, 4 October 2010
  • Sample paper and data for exploring updates
    '''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
  • Merging Papers
    [[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 f
    5 KB (837 words) - 17:43, 16 August 2010
  • WormBase Model:Analysis
    Reference ?Paper XREF Describes_analysis ...XREF Conducted // not always the same as the author of the paper - eg Erich running OrthoMCL
    1 KB (104 words) - 10:38, 10 August 2010
  • Subsequent Phenotype2GO Uploads to Postgres
    ...'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 annotatio
    674 bytes (110 words) - 19:07, 5 November 2014
  • Dumping Script
    ...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 pa
    2 KB (329 words) - 15:21, 7 August 2014
  • Getting Papers into WormBase
    ***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
  • Outstanding Model questions
    "Paper" tag becomes "Reference"
    166 bytes (25 words) - 15:02, 5 March 2011
  • Instructions for curators
    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
  • Genetics Paper Pipeline
    ...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
  • Gazette articles
    Back to [[Entering New Paper Objects]]
    174 bytes (26 words) - 23:17, 13 August 2010
  • Acceptance to first-pass
    ...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
  • WBConfCall 2014.04.03-Agenda and Minutes
    * 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, method
    2 KB (344 words) - 16:30, 3 April 2014
  • Textpresso related forms
    *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 o
    1 KB (246 words) - 04:38, 13 October 2010
  • Papers that use GO - 2015
    *Paper uses GO annotation for C. elegans GPCRs to identify receptors, and their hu
    310 bytes (43 words) - 19:43, 29 February 2016
  • Citace upload report
    ...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
  • What to do about large-scale papers
    Back to [[Paper Pipeline]]
    343 bytes (52 words) - 12:24, 5 January 2010
  • Phenote .obo files and where they come from
    #[Transgene/Summary/Paper Connections]
    313 bytes (41 words) - 20:45, 24 September 2010
  • WormBase Model:Antibody
    // Summary records the whole description extracted from paper // Other_name holds the antibody's name appeared in the paper, such as MH27
    3 KB (318 words) - 00:53, 7 December 2010
  • Erratum in and Erratum for
    Back to [[Paper Pipeline]] since the objects are associated with the original paper, WBPaper00004137. I don't know who
    2 KB (248 words) - 22:57, 13 August 2010
  • Caltech documentation
    *[[Gene-Paper Associations]] *[[Paper Pipeline]]
    3 KB (325 words) - 17:36, 25 April 2023
  • Author Curation
    2. Manually via author-paper verification Back to [[Paper Pipeline]]
    1,002 bytes (141 words) - 23:09, 30 April 2011
  • New Paper Model - Model and Changes to Pipeline
    Back to [[Paper Pipeline]] History Merged_into UNIQUE ?Paper XREF Acquires_merge
    10 KB (928 words) - 18:34, 2 May 2011
  • WBConfCall 2023.11.16-Agenda and Minutes
    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, paragra
    2 KB (267 words) - 17:43, 16 November 2023
  • WBConfCall 2017-08-03-Agenda and Minutes
    == 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
  • WormBase-Caltech Weekly Calls 2009
    *Discussion of allele-paper connections **Alleles get associated with a paper if there is phenotypic or molecular data
    3 KB (407 words) - 01:16, 19 February 2011
  • WS271 Models.wrm
    * New ?Paper Type for WS271 MODELS
    395 bytes (55 words) - 11:59, 15 April 2019
  • WBConfCall 2019.02.07-Agenda and Minutes
    ...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
  • Adding pmid Identifier to Paper Object
    '''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
  • Rnaseq library details
    Reference ?Paper XREF Rnaseq_library // add this to ?Paper
    3 KB (252 words) - 16:46, 9 January 2014
  • Invalid PMIDs in postgres and WormBase
    ...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
  • Using the Paper Editor
    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 make
    7 KB (1,204 words) - 18:58, 30 June 2014
  • 100209 seqchange
    ! 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
  • Foreign Characters in Author Names from PubMed
    Back to [[Paper Pipeline]]
    375 bytes (57 words) - 13:44, 12 May 2011
  • WS223 Models.wrm
    ?Paper > Reference ?Paper XREF Picture
    3 KB (354 words) - 11:08, 3 December 2010
  • WBConfCall 2021.08.05-Agenda and Minutes
    == Genetics paper == Sian Gramates - coordinating the FlyBase paper
    2 KB (298 words) - 16:32, 5 August 2021
  • UniProt Paper - Gene - Data Type
    * 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
  • Website:Version 1.0
    # '''Add Zotero support to the Paper page; others? CiteULike? Endnote? Mendely?''' ===Paper===
    2 KB (275 words) - 15:30, 11 January 2011
  • (1 paper)
    ! [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
  • WormBase Model:Expression cluster
    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
  • (10 papers)
    ! [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
  • Alliance - migrating WormBase papers to Alliance ABC
    ** During the call earlier we talked about the ?Paper model having *** Author ?Author XREF Paper #Affiliation
    3 KB (492 words) - 18:48, 17 March 2021
  • General specifications
    location of files on Textpresso for retrieving paper titles and abstracts paper identifier mapping file
    2 KB (204 words) - 19:18, 17 November 2011
  • WS233 Models.wrm
    ===='''?Paper'''====
    2 KB (260 words) - 11:11, 27 July 2012
  • WBConfCall 2021.05.20-Agenda and Minutes
    == WB Genetics paper update ==
    2 KB (299 words) - 16:04, 20 May 2021
  • WormBase-Caltech Weekly Calls November 2021
    === Migrating Paper Pipeline to Alliance === ...-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
    2 KB (314 words) - 19:19, 14 December 2021
  • Generating Initial GAF file for Upload to Postgres
    ...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 simple
    3 KB (482 words) - 21:21, 7 November 2014
  • WormBase-Caltech Weekly Calls April 2022
    *Discussion of what features are commonly used in the Caltech paper editor or otherwise wrt papers
    252 bytes (35 words) - 17:49, 12 May 2022
  • Paper Pipeline - To Do List
    '''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. -- DONE
    7 KB (1,103 words) - 18:08, 16 August 2010
  • WormBase Model:Reference
    ?Reference Reference ?Paper
    300 bytes (27 words) - 08:59, 5 October 2010
  • WormBase Model:Condition
    Reference ?Paper //Paper that defines the condition.
    2 KB (183 words) - 22:58, 6 December 2010
  • Microarray Data
    ...(2001), PNAS 98, 218-223] (SMD data from Kim laboratory's 2001 microarray paper)
    476 bytes (62 words) - 21:35, 29 November 2010
  • Topic (WBProcess) Model build
    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, ph
    4 KB (503 words) - 00:51, 7 November 2013
  • WormBase-Caltech Weekly Calls December 2016
    * 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
  • Instructions for Genetics
    ...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 curators
    6 KB (1,017 words) - 19:34, 2 December 2011
  • WBPaper00038399 GO linking comments
    ==Comments concerning GO linking of this paper== **'midbody' - GO term is wrong for this word in this paper
    3 KB (511 words) - 21:07, 1 August 2011
  • WBPaper00038523 GO linking comments
    ==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
  • WBConfCall 2021.04.15-Agenda and Minutes
    ...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
  • What are SVMs?
    ...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 use
    770 bytes (117 words) - 13:08, 20 November 2009
  • 112009 geneprod GO
    ! Paper describes chromosome binding in terms of localization.
    653 bytes (82 words) - 19:01, 10 August 2010
  • Training Set
    I need to obtain a list of curated paper IDs to validate the results. ! Ids of curated paper
    2 KB (241 words) - 17:46, 17 August 2010
  • WBConfCall 2021.03.18-Agenda and Minutes
    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
  • WBConfCall 2011.07.21-Agenda and Minutes
    - 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
  • Curation status
    ...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
  • WormBase Model:Microarray
    Reference ?Paper //Describes design of the chip
    726 bytes (57 words) - 14:42, 4 October 2010
  • WormBase-Caltech Weekly Calls December 2020
    === Hench et al paper === * Thomas Burglin would like the data from paper 00046864 to be included in WB
    4 KB (572 words) - 17:01, 13 January 2021
  • Genetics Markup by Textpresso and First Pass
    ...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
  • WormBase-Caltech Weekly Calls January 2021
    * 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
  • Specifications for source files
    #Paper database code:numerical identifier:Paper section:Sentence ID in Textpresso document:corpus_date_of_search
    2 KB (261 words) - 17:08, 16 April 2013
  • Further clarification
    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
  • WormBase Model:Expr profile
    Reference ?Paper XREF Expr_profile
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  • Overview
    ...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. Thes
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  • Project page for author first pass form
    '''Congratulations on the publication of your paper!'''<br> If your paper contains experiments on C. elegans and related nematodes, please continue w
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  • WBConfCall 2017-10-05-Agenda and Minutes
    * His paper has been submitted and is expected to be accepted soon ==NAR Paper==
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  • WormBase SVMs
    *Paper ID *Do we also want to store if a paper was used in an SVM training set?
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  • Detailed curation workflows and search scenarios
    Searches would return sentences, one page on the curation form per paper, if possible? #Paper
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  • Picture Data Model
    Reference ?Paper XREF Picture
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  • WBConfCall 2021.09.16-Agenda and Minutes
    == Genetics Paper==
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  • Paper Pipeline Scripts
    =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.
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  • WBConfCall 2021.04.01-Agenda and Minutes
    ...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 ==
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  • Unused evidence
    :paper/email EMPTY :paper/species EMPTY
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  • WBConfCall 2021.02.04-Agenda and Minutes
    * 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 a
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  • WBConfCall 2021.11.04-Agenda and Minutes
    ** 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.
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  • WormBase-Caltech Weekly Calls July 2016
    * Yesterday we (FlyBase, ZFIN, and WormBase) presented paper curation status tracking * Is there a working list of Phenologs anywhere? See Ed Marcotte's paper
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  • Random Selection of New Training Set Papers
    'Yes' means the paper has the data we'd want for training; flagged means it was flagged during ma
    1 KB (159 words) - 18:33, 16 August 2010
  • WBConfCall 2020.10.01-Agenda and Minutes
    > References ?Paper (optional XREF Species_in_paper) <s>* "paper link missing to sax-1?" help desk email from Nathalie Pujol Sept 26</s><br>
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  • WBConfCall 2020.04.01-Agenda and Minutes
    *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 ID
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  • Journal first-pass (jfp) postgres table details
    ...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.
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  • Juancarlos
    ...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.
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  • WBConfCall 2015.12.17-Agenda and Minutes
    == Science paper on NHGRI funding ==
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  • Types of Papers in WormBase (and Postgres)
    ...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 pipel
    2 KB (352 words) - 18:13, 17 August 2010
  • Release note requests
    *Number of paper-gene connections *Number of paper-RNAi connections
    2 KB (307 words) - 14:04, 7 February 2013
  • Geographic Displays
    ...includes a small geographic map displaying locations of the authors of the paper: $WORMBASE/cgi-perl/misc/paper: CGI script that contains the code segment
    4 KB (711 words) - 23:25, 13 August 2010
  • WormBase Model:Microarray experiment
    Reference ?Paper XREF Microarray_experiment
    892 bytes (72 words) - 14:43, 4 October 2010
  • WormBase Model:Database field
    ?Paper
    700 bytes (98 words) - 09:44, 4 October 2010
  • Automating dicty literature upload - Arun, Petra, Sidd
    ...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, and
    633 bytes (113 words) - 17:29, 19 April 2011
  • Annotation of Disease scripts
    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
  • WormBase Model:Anatomy function
    Reference UNIQUE ?Paper XREF Anatomy_function
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  • UserGuide:Simple Search
    ...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. For
    2 KB (399 words) - 18:32, 17 August 2010
  • Jfp postgres table details
    ...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
  • Feature Requests
    ...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 make
    6 KB (1,024 words) - 23:02, 13 August 2010
  • WBConfCall 2012.02.16-Agenda and Minutes
    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
  • Author Person
    2. - For each author of each paper not verified YES search: Paper auhor_id Author_name
    3 KB (435 words) - 20:52, 16 May 2011
  • WormBase Model:Feature
    ...t UNIQUE #Evidence //source data, <WSversion> ?Sequence pos1 pos2 Evidence(Paper/person etc. remarks) Defined_by_paper ?Paper XREF Feature #Evidence
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  • International C. elegans Meetings - UCLA
    ...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 tables
    3 KB (532 words) - 13:33, 31 March 2022
  • WBConfCall 2019.10.03-Agenda and Minutes
    == NAR paper== Todd: NAR paper was accepted, minor revisions submitted, and will be published in a few wee
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  • WBConfCall 2016.04.07-Agenda and Minutes
    * paper-by-paper or data-type oriented curation pipeline. Data-type oriented curation is mor
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  • WormBase Model:RNAi
    ...Reference UNIQUE ?Paper XREF RNAi //[070215 ar2] made reference unique so Paper sort of equates to a Study class for Will S
    3 KB (312 words) - 15:14, 15 July 2010
  • WormBase Model:Operon
    Reference ?Paper XREF Operon
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  • WormBase-Caltech Weekly Calls August 2013
    *Gene IDs can be found from original paper or data set Paper Categorization
    5 KB (850 words) - 15:32, 5 September 2013
  • (2 papers)
    ! [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
  • Contacting the Community
    # Should have paper editor tag-- pubmed_final final # Should have paper editor tag--Status valid
    13 KB (2,062 words) - 14:01, 4 August 2017
  • Textpresso Central
    **External identifiers - which ones? PMIDs, doi's, MOD paper IDs, others? **Paper Exclusion List - user supplied, from external data file, e.g. Gene Ontology
    6 KB (901 words) - 19:21, 29 November 2011
  • WormBase-Caltech Weekly Calls July 2017
    ...t object to point to then maybe a better approach is just to reference the paper like this: Null ?Paper
    6 KB (927 words) - 14:23, 10 August 2017
  • WormBase Model:Life stage
    Reference ?Paper XREF Life_stage
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  • WormBase Model:Molecule
    Reference ?Paper XREF Molecule Reference ?Paper XREF Molecule
    6 KB (543 words) - 23:29, 15 March 2016
  • Mf hmm tool
    ...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
  • Citace data assignments
    | Paper||Kimberly
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  • Micropub Pipeline
    * Generate a new WBPaper via the Paper Editor here: **Enter new paper
    9 KB (1,391 words) - 19:47, 19 April 2023
  • WBConfCall 2020.06.18-Agenda and Minutes
    *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 a
    3 KB (490 words) - 17:22, 18 June 2020
  • WormBase Model:YH
    Reference ?Paper XREF YH
    1 KB (139 words) - 09:51, 10 August 2010
  • Genotype
    Reference ?Paper XREF Genotype * Disease assertions (and relevant paper connections) will be dumped by the Disease Model Annotation OA
    5 KB (705 words) - 16:31, 16 June 2020
  • WormBase-Caltech Weekly Calls November 2011
    *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
  • WBConfCall 2024.04.04-Agenda and Minutes
    ===WormBase Paper Curation charge===
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  • WormBase-Caltech Weekly Calls August 2017
    ...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
  • WBConfCall 2017.01.19-Agenda and Minutes
    == Methods Paper ==
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  • (4 papers)
    ! [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
  • Texpresso/Author/Curator interim form
    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
  • Movie
    Reference ?Paper XREF Movie #added Oct2013 DR * Reference -> "mov_paper" WBPaperID paper ontology
    5 KB (814 words) - 18:48, 17 September 2018
  • WormBase Model:Cell group
    Reference ?Paper XREF Cell_group
    2 KB (159 words) - 11:11, 10 August 2010
  • Testing Search Results - 20130509
    *Paper
    911 bytes (147 words) - 20:11, 9 May 2013
  • AceDB classes
    * [[WormBase Model:Paper|Paper]]
    4 KB (568 words) - 11:06, 23 May 2011
  • Populating dois
    Populating dois for WormBase Paper Objects 2) Add dois to newly approved papers in the paper editor
    3 KB (466 words) - 17:00, 22 July 2014
  • Associating genes with papers
    Back to [[Paper Pipeline]]
    986 bytes (140 words) - 19:42, 10 August 2010
  • Transgene curation pipeline
    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
  • Gene - GO Curation Status
    ...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
  • WormBase Model:Strain
    Reference ?Paper XREF Strain
    1 KB (119 words) - 16:43, 11 April 2013
  • GO entity markup
    ...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 li
    13 KB (2,118 words) - 16:51, 20 September 2011
  • AceDB class-Interaction
    - One or more [is this correct?] Paper objects are specified as reference.
    1 KB (143 words) - 21:51, 11 August 2010
  • Datatypes flagged
    '''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 c
    12 KB (1,832 words) - 18:43, 11 August 2010
  • WormBase-Caltech Weekly Calls September 2017
    === NAR Paper === ...ositive or negative, otherwise the paper does not get an AFP flag for that paper
    6 KB (910 words) - 15:23, 5 October 2017
  • Model changes
    ==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
  • WBConfCall 2023.03.16-Agenda and Minutes
    * 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 format
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  • WormBase-Caltech Weekly Calls November 2015
    * 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 paper
    6 KB (926 words) - 16:49, 3 December 2015
  • WormBase Model:Expr pattern
    Reference ?Paper XREF Expr_pattern //Paper that the experiments were published.
    4 KB (497 words) - 22:42, 6 December 2010
  • WBPaper00038528 GO linking comments
    *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
  • Detailed Documentation of Form and Scripts
    ...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
  • WBConfCall 2022.01.06-Agenda and Minutes
    *Paul D. is wrapping up the final round of revisions for the GENETICS paper
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  • WBConfCall 2019.08.15-Agenda and Minutes
    3. SoBa Graph for NAR paper. Raymond will discuss with Sibyl on how to change the display.
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  • First-pass flagging pipelines
    ...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
  • WormBase-Caltech Weekly Calls March 2016
    === Adding WormBase-Parasite Paper to the Curation Pipeline (Kimberly) === *Developing new paper editor for Jane and Michael P. to approve parasite papers
    5 KB (689 words) - 15:35, 7 April 2016
  • WormBase-Caltech Weekly Calls July 2021
    ...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
  • Author first pass requests
    Textpresso scans the paper for an e-mail address based on the '@'. The first e-mail it finds is used a
    1 KB (196 words) - 19:48, 14 January 2013
  • WormBase Model:Gene regulation
    //"Reference" show which paper is the source of the data. Reference ?Paper XREF Gene_regulation //primary article that the data were published
    5 KB (514 words) - 21:15, 7 December 2010
  • WormBase-Caltech Weekly Calls February 2019
    * For paper-by-paper curators (vs. datatype-by-datatype) it's difficult to parse papers into dat * All MODS still need paper triage
    6 KB (910 words) - 16:43, 7 March 2019
  • WS225 Models.wrm
    Reference ?Paper XREF WBProcess
    2 KB (207 words) - 14:11, 4 March 2011
  • WormBase-Caltech Weekly Calls November 2013
    * 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 to
    10 KB (1,664 words) - 17:02, 4 December 2013
  • WormBase Model:Mass spec experiment
    ?Mass_spec_experiment Reference ?Paper XREF Mass_spec_experiment // Describes the experiment
    2 KB (184 words) - 08:38, 17 August 2010
  • Textpresso
    =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
  • In vitro flagging
    ...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 'activit
    1 KB (178 words) - 00:04, 2 February 2011
  • WormBase-Caltech Weekly Calls October 2016
    * 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
  • WormBase-Caltech Weekly Calls June 2012
    Paper pipeline for other species *Paper-anatomy term associations in Citace Minus; Raymond will take care of them
    6 KB (983 words) - 18:02, 12 July 2012
  • WBConfCall 2011.11.03-Agenda and Minutes
    **1- Gene regulation networks paper **2- Transcriptome paper
    4 KB (609 words) - 20:57, 3 November 2011
  • Type - mapping incoming Type
    ...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
  • WormBase Model:Cell
    Reference ?Paper XREF Cell
    2 KB (215 words) - 11:09, 10 August 2010
  • WormBase-Caltech Weekly Calls November 2018
    * 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 phenotypes
    6 KB (906 words) - 15:34, 6 December 2018
  • GSA Markup SOP
    *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 paths
    17 KB (2,790 words) - 20:50, 10 January 2017
  • WormBase-Caltech Weekly Calls July 2018
    * 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
  • Regional and Topical Meetings
    *Mapping spreadsheet fields to WB Paper Model:
    1 KB (201 words) - 16:34, 15 October 2012
  • DictyBase
    '''Review dicty Paper Pipeline and Textpressso''' '''Other Options for Paper Download'''
    3 KB (439 words) - 21:25, 6 November 2012
  • Phenote quirks and bugs/fixes to request
    ...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, 3
    6 KB (1,053 words) - 20:38, 24 September 2010
  • UserGuide:Microarray Page
    ...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 used
    1 KB (228 words) - 18:30, 17 August 2010
  • Entering WBG Articles
    *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 separ
    5 KB (761 words) - 21:04, 10 February 2012
  • WormBase-Caltech Weekly Calls October 2015
    * 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 class
    10 KB (1,475 words) - 16:57, 5 November 2015
  • Phenote Fields
    ...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 to
    12 KB (1,991 words) - 23:45, 14 February 2011
  • Example Pages
    <td>Paper</td> [http://dev.wormbase.org:8023/resources/paper/WBPaper00000031 WBPaper00000031]
    8 KB (1,190 words) - 23:28, 12 March 2012
  • Missing PMIDs
    ...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 er
    14 KB (2,344 words) - 23:02, 14 December 2011
  • WBConfCall 2013.08.01-Agenda and Minutes
    * OICR will write NAR paper this year for the Database issue.
    2 KB (232 words) - 09:58, 2 August 2013
  • WS236 Models.wrm
    ...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/project
    8 KB (1,073 words) - 15:31, 14 December 2012
  • UniProt-GOA syntax checking
    #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
  • WormBase-Caltech Weekly Calls March 2019
    *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
  • Old pipeline for disease data
    '''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
  • OA for disease term
    Reference ?Paper XREF DO_term |9 || Paper || Autocomplete obo, multivalue || '''required'''|| WBPaper00038373<br/>WBP
    8 KB (1,088 words) - 22:59, 29 July 2016
  • WBConfCall 2016.11.17-Agenda and Minutes
    *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, but
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  • Tasks
    *White paper on project
    1 KB (152 words) - 16:31, 16 June 2017
  • WebDev 2009.09.16-Agenda and Minutes
    - Finished the NAR database paper for WB
    2 KB (260 words) - 15:45, 16 September 2009
  • WormBase-Caltech Weekly Calls September 2011
    NAR Paper *Paper due at end of October
    6 KB (971 words) - 16:24, 6 October 2011
  • WormBase-Caltech Weekly Calls January 2012
    *One large scale paper omitted from upload *Need to wait until SVM paper accepted before moving those computers
    5 KB (847 words) - 17:49, 1 March 2012
  • WebDev 2009.08.12-Agenda and Minutes
    *For trial, Most mature dataset? -> from 2007 Nature paper, dosage compensation data
    2 KB (254 words) - 10:42, 12 August 2009
  • WBConfCall 2018.02.15-Agenda and Minutes
    * [https://github.com/WormBase/website/issues/6186 paper curation form] - CalTech
    1 KB (213 words) - 16:56, 15 February 2018
  • Micropublication tracker
    List of e-mails related to each paper: while curating your paper
    5 KB (693 words) - 18:45, 2 February 2017
  • 3rd International BioCurator Meeting, April 16th - 19th, 2009, Berlin, Germany
    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
  • WBConfCall 2021.07.15-Agenda and Minutes
    ...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 we
    1 KB (229 words) - 16:05, 15 July 2021
  • WormBase-Caltech Weekly Calls January 2022
    ...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
  • WormBase-Caltech Weekly Calls December 2013
    * 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 pipeline
    6 KB (823 words) - 19:38, 2 January 2014
  • WormBase-Caltech Weekly Calls September 2012
    ****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 now
    7 KB (1,074 words) - 17:19, 4 October 2012
  • Entity classes and problems
    ...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 ma
    10 KB (1,696 words) - 17:21, 25 July 2013
  • WebDev 2011.05.25-Agenda and Minutes
    paper x x x -
    2 KB (243 words) - 20:29, 25 May 2011
  • Phenote cgi wish list
    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 connections
    7 KB (1,075 words) - 21:05, 24 September 2010
  • WebDev 2009.10.14-Agenda and Minutes
    * resubmitted NAR paper
    1 KB (205 words) - 16:41, 14 October 2009
  • WS175
    ...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 attributed
    6 KB (680 words) - 10:54, 21 December 2011
  • WormBase-Caltech Weekly Calls June 2016
    * ~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 example
    8 KB (1,224 words) - 15:34, 21 July 2016
  • Curated data types
    | 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
  • Abstracts
    Back to [[Paper Pipeline]]
    1 KB (149 words) - 19:20, 10 August 2010
  • WormBase-Caltech Weekly Calls July 2013
    *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 discuss
    7 KB (1,059 words) - 15:37, 1 August 2013
  • WormBase-Caltech Weekly Calls August 2019
    === 2020 WB NAR paper ===
    5 KB (759 words) - 15:02, 11 September 2019
  • WBConfCall 2016.06.16-Agenda and Minutes
    * [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
  • WS241 Models.wrm
    Reference ?Paper XREF Movie Reference ?Paper XREF Movie
    7 KB (881 words) - 15:46, 21 November 2013
  • Phenotype2GO Analysis
    ...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
  • WormBase-Caltech Weekly Calls November 2012
    ...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 curators
    7 KB (1,123 words) - 16:39, 6 December 2012
  • WormBase-Caltech Weekly Calls August 2016
    === Parasite Paper Pipeline and Curation Status Tracking ===
    4 KB (646 words) - 17:33, 1 September 2016
  • Postgres queries
    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
  • WormBase-Caltech Weekly Calls March 2021
    * 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 data
    5 KB (777 words) - 13:18, 1 April 2021
  • WormBase Model:Rearrangement
    Reference ?Paper XREF Rearrangement
    3 KB (265 words) - 08:51, 5 October 2010
  • WS181
    Reference ?Paper XREF Describes_analysis ...erson XREF Describes_analysis // not always the same as the author of the paper - eg Erich running OrthoMCL
    8 KB (885 words) - 16:47, 21 December 2011

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