Search results

From WormBaseWiki
Jump to navigationJump to search

Create the page "Gene class" on this wiki! See also the search results found.

Page title matches

  • Gene Class Descriptions
    ===Gene Class Summaries=== ...type started in May 2011. The goal of this curation is to clarify what WB gene classes are, beyond a simple definition of the acronym itself. These summa
    4 KB (704 words) - 18:19, 28 June 2011
  • WormBase Model:Gene class
    Genes ?Gene XREF Gene_class
    648 bytes (65 words) - 12:56, 4 October 2010

Page text matches

  • WormBase Model:Gene name
    // ?Gene_name class to allow easier indexing of gene names and other names ?Gene_name CGC_name_for ?Gene XREF CGC_name
    842 bytes (93 words) - 12:59, 4 October 2010
  • WormBase Model:Multi counts
    ...e and it appears that the acedb source code doesn't look for this specific class. Poss could revise use of this class as it appears to be tied to multipoint data.
    816 bytes (100 words) - 15:47, 4 October 2010
  • AceDB classes tutorial
    |- class="datatitle" ! Class
    2 KB (281 words) - 21:51, 11 August 2010
  • WS227 Models.wrm
    Map class Gene class
    3 KB (306 words) - 10:00, 26 October 2011
  • WS248 Models.wrm
    == GO_annotation class == This class captures Gene::GO associateions and additional meta data associated with a curation event
    3 KB (337 words) - 16:15, 19 February 2015
  • WormBase Model:Database field
    This Tiny class appears to have moved on from it's original remit, it is used whenever/wher ?Gene
    700 bytes (98 words) - 09:44, 4 October 2010
  • WBConfCall 2022.05.05-Agenda and Minutes
    == Display of Gene Name Evidence == * We were contacted by a user who felt our gene name evidence displayed in the Overview widget is misleading/wrong
    942 bytes (149 words) - 16:13, 5 May 2022
  • Design Specs: Evidence Handling
    $data{$type}{$evidence}{class} = lc($class) if(defined $class); ==use it in each class module==
    2 KB (265 words) - 21:11, 3 January 2012
  • WS225 Models.wrm
    This cycle we see the introduction of the WBProcess class Class Addition:
    2 KB (207 words) - 14:11, 4 March 2011
  • Data Model
    ...lasses. Numbers next to each name are the number of items contained in the class/subclass. ...the class/subclass name will open the ''QueryBuilder'' on that particular class.
    1 KB (209 words) - 03:18, 13 November 2018
  • WormBase Model:Locus
    This is what's left over from the splitting of the class into CDS Pseudogene Transcript Needs a good cleanup and probably the removal of this class.
    2 KB (193 words) - 14:28, 4 October 2010
  • WormBase Model:3d data
    // A protein structure class which will store data from the NESGC Gene ?Gene XREF 3d_data
    2 KB (133 words) - 09:56, 10 August 2010
  • Linking To WormBase
    ...dentifier which is usually, but not invariably, a human-readable name. The class describes the type of the object, such as "Sequence" or "Protein. For example, the cell ADAR has a name of "ADAR" and a class of "Cell".
    6 KB (1,087 words) - 15:07, 19 June 2014
  • Website:MobileRouter
    ...rch, we query the app with '''#search/className/query'''. Example: #search/gene/unc-26 ...ew a wormbase object, we use an hash with the following format: '''#object/class/WormBaseID'''
    1 KB (193 words) - 15:28, 19 June 2014
  • WBConfCall 2015.08.06-Agenda and Minutes
    *Function vs Mutant Phenotype Gene Classes - Submissions to NCBI and EBI *see email thread: Function vs. mutant phenotype gene classes
    2 KB (329 words) - 17:10, 6 August 2015
  • WS247 Models.wrm
    == Analysis class - Gary == == GO_annotation class - Kimberly ==
    5 KB (663 words) - 16:47, 5 December 2014
  • Gene Class Descriptions
    ===Gene Class Summaries=== ...type started in May 2011. The goal of this curation is to clarify what WB gene classes are, beyond a simple definition of the acronym itself. These summa
    4 KB (704 words) - 18:19, 28 June 2011
  • WormBase Model:Variation name
    ...name Other_name_for ?Variation XREF Other_name // main reason for this class ...Public_name_for ?Variation XREF Public_name // the main name for a gene
    309 bytes (39 words) - 09:49, 10 August 2010
  • WormBase Model:WBProcess
    // WBProcess class Model - Proposed by Karen Yook WS225 // Connects to: ?Gene
    3 KB (275 words) - 01:07, 6 February 2014
  • Interaction Display in the Gene Page
    ...mber of interaction types (regulation, predicted, etc.). Objects in the YH class are of Y2H and Y1H types, and interactors in these interactions are grouped The interaction display in the gene page aims to provide a consolidated compact view of the interaction objects
    2 KB (328 words) - 23:39, 13 August 2010
  • WS237 Models.wrm
    ===?Accession class retirement phase 2=== Database ?Database ?Database_field ?Accession (XREF ?Class Tag)
    3 KB (475 words) - 14:53, 19 February 2013
  • WS250 Models.wrm
    Version UNIQUE Text // store "Gene Ontology releases/2015-06-13" as single value. Thomas input suggests: UNIQUE for single value (most notable Gene, GO_Term, and GO_Code)
    3 KB (433 words) - 08:32, 22 June 2015
  • WebDev 2011.02.16-Agenda and Minutes
    == 5. March 1st Milestone review: Class implementation (Norie, Adrian; 15 minutes) == * Try gene as search subject
    1 KB (140 words) - 21:53, 16 February 2011
  • WormBase Model:Anatomy function
    // Anatomy_function class for Raymond // ?Gene and still give some information about the experiment itself.
    1 KB (119 words) - 10:41, 10 August 2010
  • WS243 Models.wrm
    > Reflects_endogenous_expression_of ?Gene * Model change to track the Laboratory responsible for a gene class
    2 KB (253 words) - 14:58, 13 March 2014
  • UserGuide:General Description
    ...elected class will appear as the search result. For example: if you select class "Cell", and type nothing in search box, all C. elegans cells will appear in ...itive and space sensitive. You can search for a certain class such as "Any Gene" or "Author", or search for "Anything", which will return related objects f
    2 KB (416 words) - 01:03, 22 July 2013
  • Release note requests
    **through RNAi observed phenotype (ignore phenotype not observed for this class) ...ization efforts with large scale sequencing projects that do not focus on gene-phenotype analysis.
    2 KB (307 words) - 14:04, 7 February 2013
  • Data mining:AQL tutorial
    select a, b, b->gene, e->mountain from a in class pcr_product, b in a->overlaps_cds, e in a->expr_profile->expr_map
    834 bytes (137 words) - 15:09, 16 June 2011
  • WormBase Model:Rearrangement
    // ?Rearrangement class // or perhaps there should be another class Complex_Rear that refers to
    3 KB (265 words) - 08:51, 5 October 2010
  • WS241 Models.wrm
    ===?Person class=== ==?Protein Class==
    7 KB (881 words) - 15:46, 21 November 2013
  • AceOjbect Redesign Page
    {| border="1" class="wikitable" |No API needed at this time; partner class of Gene and possibly Variation, Rearrangement, Locus
    12 KB (1,559 words) - 18:14, 15 June 2011
  • WS236 Models.wrm
    === * General housekeeping - ?Accession class === ?Accession class retirement phase 1
    8 KB (1,073 words) - 15:31, 14 December 2012
  • WormBase Model:Paper
    // ?Paper class - krb 040223 // ?Paper class - krb 040223
    5 KB (471 words) - 16:07, 4 October 2010
  • Specifications for data submission to the Alliance
    {|Class="wikitable" ! !!Acedb Tags in Annotation <br/> (From ?Disease_model_annotation class)!!Primary Object!!Number of Objects<br/>with annotations!!JSON Objects
    2 KB (318 words) - 17:43, 26 October 2023
  • Jdmswong sandbox
    === Use case: How do I find all coding sequences for a gene? === ...del/genomic_model.xml model], find the gene class ( text find <class name="Gene" ).
    3 KB (330 words) - 18:37, 8 May 2013
  • Design Specs: Application Request Flow
    This is the base class for Controllers. Here I have dumb examples. All they do is return the avai ...ook at sub page(). This action matches the URL reports/*/*. It expects a class and a name of an object. From there, it fetches the object from the API, fi
    3 KB (575 words) - 18:47, 11 August 2010
  • UserGuide:Nomenclature nematode
    An accepted system of gene nomenclature was established for the nematode ''Caenorhabditis elegans'' in ...matodes, some of which are being curated by WormBase. For these organisms, gene naming will also be supervised by WormBase, in order to maximize consistenc
    6 KB (977 words) - 19:43, 14 June 2011
  • WBConfCall 2014.01.09-Agenda and Minutes
    ...models are meant to allow the incorporation of phylogenetic profile-based gene clusters created by <br> I would like to propose a new model class to hold information about
    2 KB (358 words) - 14:03, 13 January 2014
  • Issues-4/2/2013
    === 954: Gene Summary - Overview should show Dead genes which have been Merged_into anoth * TODO: to add link to gene again, push to staging when this is done
    1,009 bytes (150 words) - 18:13, 2 April 2013
  • WormBase Model:RNAi
    // ?RNAi class Inhibits Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)
    3 KB (312 words) - 15:14, 15 July 2010
  • Community Curation
    * '''Gene/Sequence Links''' * '''New Gene Class Name Proposal'''
    1 KB (165 words) - 15:47, 10 April 2015
  • WormBase Model:Transcript
    // ?Transcript class - krb 021126 ...fo DB_remark ?Text #Evidence // was missing from first draft of Transcript class krb
    4 KB (350 words) - 09:32, 17 June 2013
  • WBConfCall 2012.08.16-Agenda and Minutes
    Remove the XREF connection between the ?Laboratory class and the ?Variation class as this is a heavy weight connectivity tag for the large projects that real .../github.com/WormBase/website/issues/407 issue 407] "Error message in ran-1 gene interactions"
    2 KB (294 words) - 16:14, 16 August 2012
  • Site Map
    *[http://www.wormbase.org/db/searches/class_query WormBase Class Browser] *[http://www.wormbase.org/db/gene/gene Gene Report]
    3 KB (374 words) - 18:22, 9 March 2020
  • WormBase Model:Strain
    // ?Strain class Contains Gene ?Gene XREF Strain
    1 KB (119 words) - 16:43, 11 April 2013
  • WBConfCall 2014.02.20-Agenda and Minutes
    # tkr gene class lab association (from Peter Barrett, Tue, February 18, 2014, https://github # C06A1.4 link to sequence (gene + nt) does not work. (from Alexandra Bezler, Thu, February 20, 2014, https:
    2 KB (312 words) - 16:36, 24 February 2014
  • WormBase Model:Operon
    // ?Operon class - [010928 dl] Contains_gene ?Gene XREF Contained_in_operon #Trans_splice_leader
    1 KB (120 words) - 09:24, 10 August 2010
  • WormBase Model:Gene
    // ?Gene class - krb ?Gene Evidence #Evidence
    7 KB (712 words) - 10:40, 4 October 2010
  • Query Builder
    ...y clicking the name of the class in the [[Data Model]]. By clicking on the class name, it will bring up the builder interface shown below. ...ll ask for input regarding the constraint to be applied. If, for instance, Gene Name is selected, the dialog will ask for a match (=) or not (!=), or some
    2 KB (346 words) - 21:00, 13 November 2018
  • Design Specs: API
    Fetch other genes that the public name of the current gene might refer to. my $desc = 'proteins related to gene'; # skip variable assignment unless necessary
    9 KB (1,048 words) - 14:59, 15 February 2011
  • Specifications for a GAF for gene-life stage data
    Format: The gene association file is a 17 column tab-delimited file, where 11 columns have t {|Class="wikitable"
    2 KB (205 words) - 09:57, 28 March 2014
  • WormBase-Caltech Weekly Calls May 2020
    === Genotype class === ===Genotype class===
    5 KB (701 words) - 15:38, 4 June 2020
  • WormBase Model:Map
    Lots of unused tags, but acedb internal class. // min, max - else min, max gene/locus
    2 KB (208 words) - 14:36, 4 October 2010
  • WS228 Models.wrm
    ...ee 4 simple changes/additions and the re-working of the Expression_cluster class. ?Gene
    2 KB (199 words) - 13:31, 19 August 2011
  • WS246 Models.wrm
    1) Automated_descriptions in the ?Gene class < // Explination about class/objectcount limits
    3 KB (413 words) - 15:51, 18 September 2014
  • Citace upload report
    ...aceperl query to get at the actual annotation rather than a straight data class object number. |'''Data class/type'''||'''Curation focus'''||'''Postgres Tables'''<br>([[all OA tables |
    4 KB (580 words) - 18:13, 6 October 2017
  • WormBase Model:GO term
    // ?GO_term class modified 19/09/01 dl Gene ?Gene XREF GO_term // will this replace CDS? [040203 krb]
    2 KB (183 words) - 13:25, 4 October 2010
  • WormBase Model:Position Matrix
    //Position_Matrix class Bound_by_gene_product ?Gene XREF Product_binds_matrix #Evidence //Addition by Gary Williams
    1 KB (125 words) - 15:01, 4 October 2012
  • Phenote .ace citace upload
    ...s from phenotype annotations are added to the references on the respective gene page. Gene WBGene00000898
    5 KB (749 words) - 19:47, 17 May 2018
  • WormBase Model:Expression cluster
    // ?Expression_cluster class Gene ?Gene XREF Expression_cluster #Evidence //Igor: populated during build
    2 KB (177 words) - 22:50, 6 December 2010
  • WS186
    ...map_positions.WS186.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS186.gz - list of all current gene identifiers with CGC & molecular names (when known)
    6 KB (683 words) - 05:51, 3 April 2008
  • WormBase Model:Microarray results
    // ?Microarray_results class Gene ?Gene XREF Microarray_results #Evidence // should be mapped during the bu
    2 KB (152 words) - 14:44, 4 October 2010
  • AceDB classes
    To display the current model of any class, include the following text in your documentation: try this URL, replacing CLASS_NAME with the class of your choice
    4 KB (568 words) - 11:06, 23 May 2011
  • WormBase-Caltech Weekly Calls December 2014
    === Institution tag in ?Person class === * Do we want to create an ?Institution class? Do we want an ?Affiliation class?
    4 KB (633 words) - 19:09, 6 January 2015
  • User Guide
    ## [[UserGuide:Gene_Ontology|Gene Ontology]] ## [[UserGuide:Gene_Page|Gene Page]]
    3 KB (338 words) - 17:04, 6 August 2019
  • WBConfCall 2018.12.20-Agenda and Minutes
    ** Gene naming request; not sure if Tim has replied ** Paper-gene connections; Kimberly responded; can we close?
    3 KB (415 words) - 15:31, 24 December 2018
  • Website:Development Milestones
    ...readsheets.google.com/a/wormbase.org/ccc?key=tygSYCz49YW5hyCcYMHUZ1Q#gid=2 Class conversion matrix] *** Search mechanism; multi-class
    3 KB (378 words) - 20:23, 2 March 2011
  • WBConfCall 2020.02.20-Agenda and Minutes
    ...a is not included in the descriptions, there may be false negatives in the gene description set ...ain condition was generally not thought to be sufficient criteria to say a gene has a function
    5 KB (821 words) - 22:36, 20 February 2020
  • WormBase-Caltech Weekly Calls October 2020
    === Gene association file formats on FTP === * WormBase has a ?Transcription_factor class that is currently underutilized
    6 KB (861 words) - 19:23, 5 November 2020
  • BASIC PROTOCOL 6: SEARCHING FOR GENE PRODUCTS WITH PARTICULAR SEQUENCE MOTIFS
    ...ne whose protein product is known to be in the class of interest. Find its Gene page by a standard search (see Basic Protocol 3). Click from there to its P ...ein, core." The motif has 17 associated proteins; in cases where a motif's gene has a classical three-letter name, this is shown.''
    2 KB (279 words) - 20:01, 11 August 2010
  • Website:Molecule Object Widget Requirements Specification
    ...way to find a list of molecules that have been shown to interact with your gene of interest. Likewise, starting at a Molecule page, there is not simple wa
    1 KB (209 words) - 19:57, 25 July 2012
  • GFF Release Data and Changes
    {| class="wikitable" * gene:WormBase
    5 KB (723 words) - 19:36, 29 August 2013
  • Importing Protein Structure Data
    ...proteins (Wormpep) and they are displayed in the context of the Wormbase gene page. // Found 14876 objects in this class
    3 KB (408 words) - 23:36, 13 August 2010
  • WBConfCall 2012.02.02-Agenda and Minutes
    * only gene-gene or TF-gene/feature-gene/feature-TF too? // ?Phenotype_info Class
    8 KB (879 words) - 09:32, 3 February 2012
  • WormBase Model:Sequence
    This is a huge class with many deprecated elements. // ?Sequence class
    12 KB (1,258 words) - 09:29, 5 October 2010
  • WormBase Model:Antibody
    // XREF from ?Antibody to ?CDS class will be added after ?CDS is integrated // No connection to CDS is required - just Gene is fine
    3 KB (318 words) - 00:53, 7 December 2010
  • WBConfCall 2018.11.15-Agenda and Minutes
    ===Gene description package=== ...rk is being done on the Name Service? Will it replace the modelling of the Gene or some other classes in Datomic? Will it become the primary database?
    2 KB (323 words) - 18:24, 15 November 2018
  • WormBase-Caltech Weekly Calls April 2011
    *Working on concise descriptions of gene classes *Inconsistencies/discrepancies of gene class names
    7 KB (1,103 words) - 18:28, 5 May 2011
  • WormBase-Caltech Weekly Calls May 2019
    * To implement on Gene pages. One vs. Five widgets? * Juancarlos working on implementing SObA widgets on gene pages (maybe for WS271 or WS272?)
    6 KB (911 words) - 17:13, 6 June 2019
  • WormBase-Caltech Weekly Calls September 2018
    === Genotype class === ...ocument to draw up ?Genotype class and make appropriate changes to ?Strain class
    9 KB (1,368 words) - 15:27, 4 October 2018
  • WS214
    ...map_positions.WS214.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS214.gz - list of all current gene identifiers with CGC & molecular names (when known)
    6 KB (709 words) - 16:49, 21 December 2011
  • Updating ontology (.obo) files for the OA
    Gene ontology: http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology *gene association
    10 KB (1,644 words) - 18:48, 13 August 2020
  • Website:View
    classes/ // class-specific templates gene/ // widget templates specific for the gene class
    5 KB (687 words) - 14:10, 19 June 2014
  • Example Pages
    <tr><th>Class</th><th>Sparsely Populated</th><th>Densely Populated</th></tr> <td>Gene*</td>
    8 KB (1,190 words) - 23:28, 12 March 2012
  • WBConfCall 2013.11.21-Agenda and Minutes
    '''1) ?Person class''' '''4) ?Protein Class'''
    6 KB (909 words) - 21:56, 21 November 2013
  • Entity classes and problems
    http://www.wormbase.org/db/get?name=X;class=Y Currently we are forming URLs based on public names versus object class ID's. These links are redirected to the correct page, which is the URL bas
    10 KB (1,696 words) - 17:21, 25 July 2013
  • Dumping Script
    The dumping script will check for any dead gene IDs attached to papers and comment them out of the .ace file until they are ..., Journal, Volume) and some fields/tags are multi-value (e.g., Identifier, Gene). The full list of fields classified according to single- or multi-value i
    2 KB (329 words) - 15:21, 7 August 2014
  • WormBase-Caltech Weekly Calls July 2021
    * ~100,000 alleles in Postgres; ~70,000 don't have a gene connection * Would Hinxton be willing to take WS-mapped allele-to-gene associations and populate GeneACE with associations not already in there?
    5 KB (670 words) - 16:00, 5 August 2021
  • UniProt Paper - Gene - Data Type
    The Categories would be gene-specific and we will supply information for: * Remove redundant gene-paper associations
    4 KB (556 words) - 12:45, 21 May 2019
  • WormBase Models
    {| border="1" class="wikitable" ! Class
    16 KB (2,207 words) - 23:06, 9 January 2014
  • WormBase Model:Transgene
    Historical_gene ?Gene #Evidence Promoter Driven_by_gene ?Gene XREF Drives_Transgene
    13 KB (1,341 words) - 20:12, 22 September 2015
  • WS181
    ...map_positions.WS181.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS181.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    8 KB (885 words) - 16:47, 21 December 2011
  • WormBase Model:Feature
    // Feature class Associations Associated_with_gene ?Gene XREF Associated_feature #Evidence // richard
    4 KB (394 words) - 08:39, 16 September 2014
  • WormBase Model:CDS
    // ?CDS class - To store all coding genes Genetic_code UNIQUE ?Genetic_code // needed for one gene with selenocysteine!
    4 KB (410 words) - 17:08, 17 August 2010
  • WBConfCall 2016.01.21-Agenda and Minutes
    ** changing the Person class to add a PI tag would be possible * Gene Classes vs Biotypes from Sequence Ontology Terms - specificity/uniqueness/p
    1 KB (207 words) - 09:45, 22 January 2016
  • WebDev 2011.04.06-Agenda and Minutes
    * GFF3 file issues -- names in objects; need info on the gene level (LS) * class level disambiguation
    1,022 bytes (140 words) - 09:36, 7 April 2011
  • Coding standards
    CSS variable names SHOULD follow the same conventions as public class variables. Private class variables should be written using lowercase with a preceding underscore):
    6 KB (950 words) - 15:36, 19 June 2014
  • WBConfCall 2019.10.03-Agenda and Minutes
    * which class of object do we consider them to be * Chris: could we have them parented by locus, as a distinct class of transcript?
    4 KB (645 words) - 23:43, 3 October 2019
  • Design Specs: Database Connectivity
    ...ene.t http://bitbucket.org/tharris/wormbase/src/tip/t/WormBase/API/Object/Gene.t ok 3 - The object isa WormBase::API::Object::Gene
    6 KB (980 words) - 18:48, 11 August 2010
  • WBConfCall 2013.11.07-Agenda and Minutes
    * ?Person class - Database tag added for ORCID ...ne_cluster - Karen would like to use this underused class for phylogenetic gene clusters
    8 KB (1,246 words) - 15:52, 12 November 2013
  • WBConfCall 2022.09.08-Agenda and Minutes
    ...begin to annotate the orthologs, and also adopt their methods for de-novo gene finding in C. elegans. Do we know any researcher who'd like to do some of t ...n. None of the paragraphs mention any work or plan for migrating that data class to Alliance - is that right? Some overview is mentioned in the introductory
    2 KB (326 words) - 16:00, 8 September 2022
  • WS174
    ...map_positions.WS174.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS174.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    8 KB (938 words) - 10:54, 21 December 2011
  • WBConfCall 2012.12.06-Agenda and Minutes
    1 * General housekeeping - ?Accession class 2 * Transposon gene reactivation - Paul
    5 KB (752 words) - 18:55, 6 December 2012
  • WormBase-Caltech Weekly Calls February 2020
    === ?Genotype class model === * WormMine now returning double the gene count for C. elegans genes because of incorporation of newest VC2010 assemb
    4 KB (605 words) - 15:21, 3 March 2020
  • WormBase Model:Variation
    //Variation class Affects Gene ?Gene XREF Allele #Molecular_change //#Molecular_change mh6 define prec
    8 KB (853 words) - 23:50, 16 April 2014
  • WormMine
    {| class="wikitable" border="1" | Orthology || ACeDB gene class (Ortholog and Ortholog_other tags) and there is also a OICR created flatfil
    15 KB (2,088 words) - 16:16, 15 October 2020
  • WBConfCall 2012.05.03-Agenda and Minutes
    class. Does anyone have a reason for keeping the "Author" tag in the RNAi class
    4 KB (599 words) - 00:25, 4 May 2012
  • WormBase Model:Gene regulation
    // ?Gene_regulation class - Wen 05082003// // Gene regulation model describes the expression pattern in different genetic back
    5 KB (514 words) - 21:15, 7 December 2010
  • Further clarification
    ..., including ASER; We analyzed a dataset of 52 genes that based on reporter gene analysis are expressed in ASE (ETCHBERGER et al.2007)(Supplementary Table 1 of where the gene is expressed, so they only try genes that were studied and published before
    3 KB (582 words) - 23:08, 13 August 2010
  • WormBase Model:Clone
    // ?Clone class Positive Positive_gene ?Gene XREF Positive_clone
    10 KB (1,176 words) - 22:24, 18 March 2014
  • Rnaseq library details
    // ?Rnaseq_library class - gw3 Jan 2014 ...// Ribo-zero treated to reduce the amount of ribosome gene transcripts
    3 KB (252 words) - 16:46, 9 January 2014
  • WormBase-Caltech Weekly Calls March 2014
    ...ssing how to handle plasmids/vectors, whether they should go in the ?Clone class (there is precedence) ...rs) to the ?Clone class which can then be referenced within the ?Construct class
    8 KB (1,218 words) - 17:46, 2 April 2014
  • 100209 seqchange
    {| class="wikitable" border="1" ! First detailed molecular characterization of let-721 gene and protein.
    2 KB (272 words) - 18:58, 10 August 2010
  • WBConfCall 2017.03.16-Agenda and Minutes
    ...links for accession numbers are text fields, others point to the accession class * In WS258 adding gene classes as a class to WormMine
    3 KB (493 words) - 16:08, 16 March 2017
  • WormBase-Caltech Weekly Calls November 2019
    === ?Genotype class === === Gene comparison SObA ===
    5 KB (747 words) - 16:31, 5 December 2019
  • WS213
    ...map_positions.WS213.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS213.gz - list of all current gene identifiers with CGC & molecular names (when known)
    6 KB (764 words) - 16:45, 21 December 2011
  • Expression Cluster
    ...WormBase, we need to map all the entities into WormBase IDs. These include gene ID, anatomy term, life stage, and molecule ID for chemicals used in the exp <br>Sample Supplementary file for the differentially expressed gene list. This is an example of a single-cell RNASeq study
    4 KB (406 words) - 18:13, 25 April 2023
  • WormBase Model:Phenotype info
    // ?Phenotype_info Class Caused_by ?Gene #Evidence
    5 KB (352 words) - 17:20, 25 September 2015
  • WS216
    ...map_positions.WS216.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS216.gz - list of all current gene identifiers with CGC & molecular names (when known)
    7 KB (818 words) - 11:10, 21 December 2011
  • Caltech documentation
    *[[Automated gene descriptions 2.0]] *[[Gene Class Descriptions]]
    3 KB (325 words) - 17:36, 25 April 2023
  • Cosmids/YACs
    {| border="1" class="wikitable" {| border="1" class="wikitable"
    12 KB (1,857 words) - 16:21, 5 January 2021
  • WormBase Model:Protein
    // ?Protein class Ortholog_gene ?Gene XREF Ortholog_other #Evidence //[change Ortholog others to link to proteins
    2 KB (305 words) - 08:49, 5 October 2010
  • Local installation of WormBase
    ...omehwere over the Atlantic or explore expression patterns of your favorite gene family at your local coffee shop. ...requires that one be familiar with Unix/Linux and have access to a server-class machine. This requires significant time and effort upfront, and some time e
    2 KB (281 words) - 17:30, 16 August 2010
  • Phenote quirks and bugs/fixes to request
    == Unrepeatable weirdness&lt;span class == ...of the entry fields? --[[User:Kyook|kjy]] 11:49, 18 March 2008 (EDT)<span class="Apple-style-span" style="font-style: italic;">
    6 KB (1,053 words) - 20:38, 24 September 2010
  • WBConfCall 2013.02.07-Agenda and Minutes
    ***Accession class retirement continues ...t users. why not include a link to wormviz on the expression page for each gene?"
    2 KB (383 words) - 11:59, 15 February 2013
  • Unused evidence
    :antibody/gene (2753 values, 0 evidence) :cell/other-name (919 values, 0 evidence -- Raymond suggests killing this class?)
    7 KB (604 words) - 18:21, 11 November 2014
  • WBConfCall 2020.03.05-Agenda and Minutes
    * The following 3 items are linked and the Gene has been named and a new lab created: ** Has anyone replied to Montserrat Elías regarding naming of same gene, Y53C10A.5? - This name has been agreed by Tim S. and the issue can be clos
    5 KB (857 words) - 14:36, 9 March 2020
  • WBConfCall 2016.04.21-Agenda and Minutes
    * Yeast, worm, mouse, rat, gene ontology (missed any ?) discussing forming a consortium, deciding how deep. * ZFIN uses this format: three letter database- class-number, ex: ZDB-GENE-980526-388,ZDB-TSCRIPT-110325-1492, ZDB-MRPHLNO-110614-1, ZDB-FISH-150901-1
    5 KB (732 words) - 14:46, 29 April 2016
  • WS230 Models.wrm
    Ace2SO class: gives a mapping from Acedb objects to their SO terms. SO_parent_obj_tag - Tag pointing to semantic parent of this object, e.g. "Gene"
    3 KB (368 words) - 10:15, 1 February 2012
  • BASIC PROTOCOL 2: PERFORMING A DATABASE SEARCH
    ...irectly to the Web page for that record (it will automatically do this for Gene pages). However, it will usually instead have 0 or ‚â•2 results. In th ...e database for the search from the "Search for" pull-down menu (e.g., "Any Gene"; (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png)), or check
    3 KB (545 words) - 19:56, 11 August 2010
  • WBConfCall 2018.01.04-Agenda and Minutes
    ** Affect more than one gene * Only a simple change for the Gene_class class to avoid two Description fields
    2 KB (327 words) - 16:50, 4 January 2018
  • WS221
    iii) geneIDs.WS221.gz - list of all current gene identifiers with CGC & molecular names (when known) sequences/rna - WormBase rna gene data.
    17 KB (1,758 words) - 16:47, 21 December 2011
  • WebDev 2010.11.17-Agenda and Minutes
    * Worked with Joanna from OMIM for linking from OMIM to WB, she will link to Gene reports and Disease pages class summary:
    1 KB (213 words) - 22:01, 17 November 2010
  • Model changes to capture and consolidate human disease data
    ==Gene class proposal (April 2020)== ?Gene
    32 KB (3,649 words) - 20:55, 21 May 2020
  • WormBase-Caltech Weekly Calls November 2018
    * there would be value in having a separate ?Expr_annotation class, like we did for ?GO_annotation. It might look something like this (details Class ?Expr_annotation
    6 KB (906 words) - 15:34, 6 December 2018
  • Genotype
    ...henotype curators) to annotate directly to entire genotypes, the ?Genotype class has been proposed. The decision was made that any ?Genotype object should r ...scripts to add automatically inferred gene associations from variation-to-gene mapping pipeline output
    5 KB (705 words) - 16:31, 16 June 2020
  • WS220
    iii) geneIDs.WS220.gz - list of all current gene identifiers with CGC & molecular names (when known) sequences/rna - WormBase rna gene data.
    16 KB (1,762 words) - 11:10, 21 December 2011
  • WBConfCall 2017-04-20-Agenda and Minutes
    * we should populate the PI tag in the WBPerson class * data exchange format for gene ids need to be worked out (Sybil)
    2 KB (339 words) - 16:20, 20 April 2017
  • Life Stage
    *gene regulation -Xiaodong *gene expression -Daniela
    14 KB (2,213 words) - 19:26, 12 February 2019
  • Phenotype2GO Analysis
    {| class="wikitable" ...!! Evidence Code !! Comment !! Recommend Keep Phenotype2GO Annotation? || Class of P2GO
    5 KB (825 words) - 21:25, 24 June 2013
  • WormBase-Caltech Weekly Calls October 2016
    * There's a distinction between annotating to an instance vs. to a class ...notate to higher level (cell/anatomy function) and lower level (individual gene product function)? There may be, but all of this information is valuable
    8 KB (1,289 words) - 18:11, 10 November 2016
  • WormBase-Caltech Weekly Calls October 2015
    ** So many of the tags were shared (or could be shared) with the ?Paper class * Would like community to edit manually-written and automated gene descriptions
    10 KB (1,475 words) - 16:57, 5 November 2015
  • WormBase Model:Interaction
    // ?Interaction class for Andrei WBInteraction00000001 Interactor ?Gene XREF Interaction #Interactor_info
    12 KB (1,431 words) - 19:06, 20 March 2012
  • WBConfCall 2022.09.01-Agenda and Minutes
    ** pseudo gene sequences should be on the website. Magda will investigat ...The main use case would be to link WB pages to Alliance disease section on gene pages.
    6 KB (982 words) - 16:54, 1 September 2022
  • WormBase-Caltech Weekly Calls October 2013
    ...erver for the information the browser queries: gene ontology associations, gene association files *Daniela will add a Database tag to the ?Movie class
    13 KB (1,983 words) - 16:40, 7 November 2013
  • WormBase-Caltech Weekly Calls September 2021
    ...liance is not against person pages, just not supportive of developing this class into the many ways it will be useful for us and our communities 2. CeNGEN data on Gene page for WS282. A short blog to highlight.
    2 KB (325 words) - 15:24, 7 October 2021
  • WBConfCall 2014.06.05-Agenda and Minutes
    ...ther. WB can link to ParaSite for annotation. C. elegans genes on ParaSite gene tree can link back to WB. ...ailable in the nex couple of years, need suggestions on what to include in gene tree. Paul will visit Hinxton next week and talk with Hinxton group about t
    8 KB (1,391 words) - 11:57, 6 August 2014
  • WormBase-Caltech Weekly Calls May 2017
    * GO-CAM (Gene Ontology - Causal Activity Model(ing)) * Changing Strain tag in the Phenotype class, which is used as a primary object for annotating a phenotype to, to clarif
    8 KB (1,229 words) - 15:31, 1 June 2017
  • Adding Data to a Widget (Example)
    my $gene_class = $api->fetch({ class => 'Gene_class', name => 'daf' }); (The Analysis.pm - API file of the Gene class - is in the directory lib/WormBase/API/Object/.)
    6 KB (907 words) - 18:45, 19 June 2014
  • WBGene information and status pipeline
    =Table Summarizing Former and Current Postgres Gene Information (gin_ ) Population= {| class="wikitable" border="1"
    9 KB (1,464 words) - 14:10, 29 May 2015
  • WormBase-Caltech Weekly Calls April 2018
    * Have been working on gene summaries === Essential gene lists ===
    8 KB (1,262 words) - 15:34, 3 May 2018
  • 2010.05 OICR WebDev Meeting
    * Expanded class coverage ** Gene (NdlC)
    2 KB (280 words) - 19:14, 10 August 2010
  • WS227
    ...G_SPECIES.WS227.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known) - G_SPECIES.WS227.SRA_gene_expression.tar.gz - Tables of gene expression values computed from SRA RNASeq data
    15 KB (1,738 words) - 11:20, 21 December 2011
  • Automated descriptions for C. briggsae
    *gene association file for C. brigssae: ftp://ftp.sanger.ac.uk/pub/wormbase/relea ==Template and Rules for a C. briggsae gene description==
    14 KB (1,958 words) - 20:14, 2 January 2015
  • UserGuide:RNAi Search
    ...ssible that an RNAi result of 'wild-type' ("WT") is misleading because the gene inactivated by RNAi acts in a tissue insusceptible to RNAi, or because ther ...notypes are expected to identify those genes where a substantial amount of gene activity is maternal in addition to (or rather than) zygotic.
    4 KB (720 words) - 18:31, 17 August 2010
  • Mining WormBase with Bio::DB::GFF
    ...e another, for example, finding all genes that are in an intron of another gene. Comparing syntenic regions of the C. elegans and C. briggsae genomes. You ...) genes that are contained within the intron of another named or predicted gene and print out 100 bp upstream from their 5' end:
    11 KB (1,663 words) - 17:45, 16 August 2010
  • Updating Postgres with New WS Information
    ...d are listed below. Currently, these files contain all members of a given class, regardless of species. **WSVariation.ace - used to supplement variation-gene connections not found in the nightly geneace dump; also for UniProt?
    18 KB (2,743 words) - 17:14, 16 March 2023
  • WormBase Model:Gene cluster
    This class appears to be almost unused as the added benefit tags aren't populated, jus ...UNIQUE ?Text // Information on the Gene cluster
    15 KB (1,645 words) - 18:54, 23 January 2014
  • WBConfCall 2024.01.18-Agenda and Minutes
    ...once Tim is present, probably on Feb 1st] New additions to Gene or Protein class (Structural biology ribosomal protein names) https://github.com/WormBase/we
    3 KB (432 words) - 17:19, 18 January 2024
  • WormBase-Caltech Weekly Calls June 2017
    ...working on ?Phenotype_assay (?Phenotype_experiment/?Phenotype_annotation) class model ...forward to represent the RNAi dsRNA sequence or reagent used to knockdown gene expression
    8 KB (1,213 words) - 15:29, 6 July 2017
  • Specifications for a DAF for gene-disease data
    ...our annotations Disease_relevant_gene is going to be present, pick this (Gene) as the DB Object for DAF/JSON if Strain, Variation, Transgene are all abse ...present, pick that as the DB Object for DAF, even though Disease_relevant gene is present. If more than one of these is present, then the order should be
    10 KB (1,599 words) - 18:53, 24 January 2019
  • Model changes
    ==Micropublication in ?Paper class== *Reviewers: Kimberly was proposing to create a ?Reviewer class, similar to ?Authors. This will be beneficial to elevate contributions from
    7 KB (934 words) - 19:56, 27 September 2016
  • WS173
    ...map_positions.WS173.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS173.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    6 KB (639 words) - 10:55, 21 December 2011
  • WormBase-Caltech Weekly Calls October 2019
    * [http://wobr2.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 1] * [http://wobr1.caltech.edu/~azurebrd/cgi-bin/soba_multi.cgi?action=Gene+Pair+to+SObA+Graph Prototype 2]
    13 KB (2,025 words) - 16:28, 7 November 2019
  • WormBase-Caltech Weekly Calls August 2015
    === UniProt/wormbase gene class === Goal: Provides an ontology-relationship-aware summary view of a gene's phenotype annotations.
    8 KB (1,220 words) - 16:26, 3 September 2015
  • WBConfCall 2012.07.019-Agenda and Minutes
    *Cursory gene pages for Tier II and III genes **Classification: intergenic vs. gene overlapping(?)
    4 KB (617 words) - 17:01, 19 July 2012
  • Markup excerpts
    {| class="wikitable" border="1" **'''all gene links within genomic expressions will be unmade'''
    3 KB (415 words) - 21:29, 23 July 2013
  • WS198
    ...map_positions.WS198.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS198.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    6 KB (692 words) - 16:51, 21 December 2011
  • WS203
    ...map_positions.WS203.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS203.gz - list of all current gene identifiers with CGC & molecular names (when known)
    6 KB (662 words) - 16:50, 21 December 2011
  • WormBase-Caltech Weekly Calls June 2020
    * Gene descriptions can focus on information poor genes, protein domains, etc. * Chris gave presentation to Lina Dahlberg's class about community phenotype curation
    8 KB (1,228 words) - 20:57, 14 July 2020
  • Linking script pipeline
    The entity list for '''Gene''' is formed by querying the postgres gin_ tables on tazendra, which are up and outputs a list of all gene names in file<br>
    14 KB (2,324 words) - 19:51, 9 January 2015
  • WormBase-Caltech Weekly Calls March 2011
    ...try to generate an ACEDB patch every other month, starting with the Paper class data *Rayomnd: citace 224 to 225 (for example), display done on class level
    13 KB (2,097 words) - 22:48, 7 April 2011
  • WormBase-Caltech Weekly Calls August 2014
    ...y are trying to answer when they go to the website?". When they explore a gene or protein function, what is it that they would want to see, and how? I do ...aceperl query to get at the actual annotation rather than a straight data class object number.
    6 KB (974 words) - 17:28, 3 September 2014
  • WormBoard
    {|class="wikitable" {|class="wikitable"
    16 KB (2,224 words) - 17:36, 25 August 2023
  • WBConfCall 2023.09.21–Agenda and Minutes
    ** Go through everything class by class and see what's worth doing. Find some temporary solutions if necessary. ** Gene name changes are important.
    9 KB (1,570 words) - 16:36, 21 September 2023
  • New Paper Model - Model and Changes to Pipeline
    ...?Text //we are cleaning up Journal names and considering retiring the class''' Refers_to Gene ?Gene XREF Reference #Evidence
    10 KB (928 words) - 18:34, 2 May 2011
  • WormBase-Caltech Weekly Calls January 2014
    ...o go over what more needs to be done for the construct/variation/transgene class - Main people being Mary Ann, Daniela, Chris, and Karen, others are welcome ***direct and indirect gene connections will be displayed in a list format
    10 KB (1,583 words) - 18:16, 5 February 2014
  • WormBase-Caltech Weekly Calls November 2020
    *Valerio and Ranjana still working with the GAF 2.0 files to generate gene descriptions ...probably have a meeting with Magdalena to sort out the FTP file issues for gene descriptions
    4 KB (695 words) - 14:44, 3 December 2020
  • WS197
    ...map_positions.WS197.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS197.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    6 KB (672 words) - 16:43, 21 December 2011
  • WS107
    ...map_positions.WS107.gz - Interpolated map positions for each coding/RNA gene Confirmed introns not is a CDS gene model;
    6 KB (659 words) - 11:17, 21 December 2011
  • NBC sign off documentation
    ...s has all necessary information -- /usr/local/wormbase/databases/{RELEASE}/gene * Kev thought of creating a disease class instead of putting it as text into the accession numbers. Especially since
    4 KB (583 words) - 20:22, 29 July 2011
  • Co-op Documentation
    ...nteractions widget on the Gene page ([WormBase dir]/root/templates/classes/gene/interactions.tt2) #Determines the class and widget from the url
    11 KB (1,786 words) - 14:31, 17 May 2016
  • TransgeneOme import
    ...have for each gene that has <Explore localization> data, is a table with Gene Strain image_name life_stage Annotations_by Anatomy_annotations Subcellular ...gher resolution version, does that get a new ID that gets assigned to the gene while the previous image ID association gets removed?
    11 KB (1,190 words) - 19:16, 26 September 2019
  • WS182
    ...map_positions.WS182.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS182.gz - list of all current gene identifiers with CGC & molecular names (when known)
    6 KB (716 words) - 16:48, 21 December 2011
  • FIGURE(S)
    ...y, one could pick a specific data class in the search menu (such as “Any Gene” or “Cell”; (</nowiki>http://www.wormbase.org/wiki/index. ...given gene in ''C. elegans''. Even in this excerpt, one can get summarized gene function and orthology, a list of transcripts and their experimental eviden
    19 KB (3,061 words) - 23:01, 13 August 2010
  • WS192
    ...map_positions.WS192.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS192.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    6 KB (763 words) - 10:43, 21 December 2011
  • WBConfCall 2014.09.03-Agenda and Minutes
    *Pointed them to our gene-disease association file, on the FTP site:ftp://ftp.sanger.ac.uk/pub/wormba ...n of a new tag, 'Automated_description' to 'Structured_description' under ?Gene.
    5 KB (807 words) - 18:27, 4 September 2014
  • Micropub Pipeline
    {| class="wikitable" | gene
    9 KB (1,391 words) - 19:47, 19 April 2023
  • WormBase-Caltech Weekly Calls March 2018
    ** Want to indicate, for a query gene, genes for which multiple interaction types have been observed * Adding functionality to WormMine that preserves original gene list
    11 KB (1,703 words) - 15:27, 5 April 2018
  • WormBase-Caltech Weekly Calls January 2018
    * Should we generate a ?Genotype class to capture genotypes without a known strain name? Or to capture relevant/re ** Introduction of a new ?Strain class attribute of a unique serial identifier (like WBStrain00001) would be very
    12 KB (1,930 words) - 17:12, 1 February 2018
  • WormBase-Caltech Weekly Calls March 2013
    Gene Concise Description form *Prepopulation: Display all (key?) experimental info on gene from WormBase, some Textpresso info like "ABC-1 encodes..."
    7 KB (1,047 words) - 15:34, 4 April 2013
  • Mark up policy
    '''Gene name.''' ''mpk-1'' → Gene Summary page: <http://www.wormbase.org/db/gene/gene?name=mpk-1;class=Gene><br>
    14 KB (2,365 words) - 21:14, 23 July 2013
  • WormBase Model:Molecule
    ...sion_cluster XREF Regulated_by_molecule //Added for molecule regulation of gene expression by Wen // Molecule class Model - Proposed by Karen Yook WS217
    6 KB (543 words) - 23:29, 15 March 2016
  • WS175
    ...map_positions.WS175.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS175.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    6 KB (680 words) - 10:54, 21 December 2011
  • WormBase-Caltech Weekly Calls January 2013
    *Trying to display site-of-action data on relevant gene pages *Can images be linked to sequences, rather than gene objects?
    10 KB (1,553 words) - 18:04, 7 February 2013
  • WormBase-Caltech Weekly Calls January 2012
    *BioGRID, Gene Orienteer, Interolog database, etc. *Gene Orienteer
    5 KB (847 words) - 17:49, 1 March 2012
  • WormBase-Caltech Weekly Calls December 2012
    *Complex gene information will still be best handled manually *Applying gene (GO) annotations across all species
    9 KB (1,339 words) - 19:02, 31 January 2013
  • OA forms, tables, scripts, etc
    ...ge.pl<br>sym link: /home/acedb/xiaodong/antibody/use_package.pl ||Paper<br>Gene<br>Laboratory<br> || ||Xiaodong Wang|| |concise<br>[[WormBase_Model:Gene|gene model]]||Concise Description||con_ ||/home/postgres/work/citace_upload/conc
    20 KB (3,050 words) - 21:01, 19 April 2017
  • WS226
    ...G_SPECIES.WS226.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known) - G_SPECIES.WS226.SRA_gene_expression.tar.gz - Tables of gene expression values computed from SRA RNASeq data
    21 KB (2,346 words) - 11:15, 21 December 2011
  • WS180
    ...map_positions.WS180.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS180.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    7 KB (771 words) - 10:52, 21 December 2011
  • WormBase-Caltech Weekly Calls April 2017
    * Users could specify groups of data (with checkboxes): gene IDs/names, phenotypes, orthology, etc. === Gene Ontology SObA graph ===
    7 KB (1,010 words) - 17:08, 4 May 2017
  • WBConfCall 2020.04.02-Agenda and Minutes
    * Where can i find the upstream and downstream limits for a gene? [https://github.com/WormBase/website/issues/7651 #7651] and [https://githu *Are there changes in the transgender class? Chris: not yet, might send a patch to Hinxton
    3 KB (523 words) - 11:20, 3 April 2020
  • WS170
    ...map_positions.WS170.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS170.gz - list of all current gene identifiers with CGC &amp; molecular names (when known)
    8 KB (820 words) - 10:51, 21 December 2011
  • WBConfCall 2015.06.18-Agenda and Minutes
    ** Gene Ontology annotations and enrichment tools - Kimberly Van Auken ** Contributing & editing gene concise descriptions - Ranjana Kishore
    9 KB (1,431 words) - 23:32, 23 June 2015
  • Source and maintenance of non-WBGene info
    ...peline | over here]]. This current page outlines the processing of all non gene information supplied through the dump. *gene association
    8 KB (1,375 words) - 05:12, 21 April 2020
  • WS147
    ...map_positions.WS147.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS147.gz - list of all current gene identifiers with CGC & molecular names (when known)
    7 KB (815 words) - 11:09, 21 December 2011
  • WS217
    ...map_positions.WS217.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS217.gz - list of all current gene identifiers with CGC & molecular names (when known)
    8 KB (915 words) - 11:10, 21 December 2011
  • OA and scripts for disease data
    The gene-disease OA (connected in AceDB models to ?Gene class) and the newer Disease_model_annotation data are now in the Disease OA. #'''Disease relevant gene (dis_wbgene):'''this is the causative gene of the disease, the disease_relevant_gene in ace model, DB_Object_ID in the
    36 KB (4,595 words) - 18:10, 15 March 2023
  • WormBase-Caltech Weekly Calls February 2014
    === Gene Association files === * Life stage-gene associations
    10 KB (1,485 words) - 18:08, 5 March 2014
  • Gene Interaction/archive
    ...oduct XREF Interaction #Interactor_info // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments ...Sequence XREF Interaction #Interactor_info // Sequence of the interacting gene or protein
    50 KB (5,228 words) - 15:10, 21 July 2017
  • WormBase Model:Construct
    ...a side benefit to the creation of the Construct model, we can use this new class to also capture the genomic arrays used create transgenes. Class itself is new
    20 KB (2,339 words) - 18:04, 23 September 2015
  • WBConfCall 2014.07.03-Agenda and Minutes
    1) The long awaited ?Construct class - Karen 2) Clone Class additional ?Sequence connections to remove ambiguity - Paul
    15 KB (2,374 words) - 16:00, 17 July 2014
  • OA for disease term
    In cases where there is no elegans gene to attach disease data (eg., Huntington's disease), data will be attached t Attribute_of Gene_by_biology ?Gene XREF Experimental_model
    8 KB (1,088 words) - 22:59, 29 July 2016
  • Expression pattern remodel
    ?Expr_pattern Expression_of Gene ?Gene XREF Expr_pattern #Evidence Historical_gene ?Gene #Evidence
    16 KB (1,695 words) - 08:29, 12 May 2014
  • WormBase-Caltech Weekly Calls July 2017
    * What's required for site of action? Phenotype, gene, cell/tissue where gene is introduced or removed * Will human genes link to AGR human gene pages? Gene Cards? HGNC?
    6 KB (927 words) - 14:23, 10 August 2017
  • Textpresso Central
    **Paper Exclusion List - user supplied, from external data file, e.g. Gene Ontology Annotation File (gaf) ***Use case: FlyBase CCC search using only gene names that start with CG
    6 KB (901 words) - 19:21, 29 November 2011
  • WS230
    ...G_SPECIES.WS230.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known) - G_SPECIES.WS230.SRA_gene_expression.tar.gz - Tables of gene expression values computed from SRA RNASeq data
    17 KB (1,950 words) - 09:37, 7 February 2012
  • Web2.0 Javascript use and maintenance
    search_change: search_change, // change the class search filter <div class="toggle">some hint text...</div>
    6 KB (671 words) - 16:43, 20 August 2013
  • WormBase-Caltech Weekly Calls April 2021
    * Alignment of the antibody class to Alliance: * Want gene page images for CeNGEN data; have the specifications for such images been w
    11 KB (1,782 words) - 17:55, 13 May 2021
  • Meetings
    **[C. elegans topic meeting: Development, Cell Biology, and Gene Expression](http://conferences.union.wisc.edu/cedevelopment/)**<br> {| border="1" class="wikitable"
    12 KB (1,663 words) - 16:28, 9 October 2023
  • Specifications for a Community Annotation Form
    5. ''Choose a gene'' 6.''Write a concise description for the gene you've chosen.''
    12 KB (1,838 words) - 18:16, 19 May 2015
  • Tasks in Progress
    **Set Gene as default 'Interactor Type' for Cytoscape display **[http://dev.wormbase.org:8023/species/c_elegans/gene/WBGene00018788#8--10 WBGene00018788]
    29 KB (4,254 words) - 20:25, 27 April 2012
  • All OA tables
    '''postgres tables for the Antibody class<br> dumper on tazendra at /xiaodong/antibody/use_package.pl ''' | Gene||abp_gene||multiontology||Gene||all||WBGene||gin_tables||||
    37 KB (5,333 words) - 19:07, 27 June 2019
  • WormBase-Caltech Weekly Calls September 2020
    * afp_othergenefunc (to capture gene function other than enzymatic activity) ** Automated Gene Descriptions
    7 KB (1,044 words) - 14:45, 8 October 2020
  • First-pass flagging pipelines
    {|class="wikitable sortable" | Gene Description
    15 KB (2,589 words) - 16:42, 11 January 2018
  • WormBase-Caltech Weekly Calls February 2013
    New genome assemblies and gene names across species *How do we handle independent, conflicting genome assemblies and gene models?
    8 KB (1,161 words) - 16:34, 7 March 2013
  • Phenote Fields
    ...ss retrieve to view information from the latest WS build. For alleles, the gene connection will be displayed if there is one. For rearrangements, the infor ...On the other hand, she has not curated Ex arrays, so this may be a large class of objects we will have to work with her to create.
    12 KB (1,991 words) - 23:45, 14 February 2011
  • WS222
    iii) geneIDs.WS222.gz - list of all current gene identifiers with CGC & molecular names (when known) sequences/rna - WormBase rna gene data.
    15 KB (1,647 words) - 10:06, 22 December 2010
  • WormBase-Caltech Weekly Calls May 2016
    * Made adjustments to gene name handling === Gene summaries ===
    9 KB (1,336 words) - 15:32, 2 June 2016
  • Topic pages
    =Renaming this class= * Portal for larger biomedical community into C. elegans gene function.<br>
    20 KB (3,088 words) - 19:17, 13 August 2020
  • WormBase-Caltech Weekly Calls September 2016
    * Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not ...uld we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
    9 KB (1,490 words) - 15:35, 6 October 2016
  • WS223
    iii) geneIDs.WS223.gz - list of all current gene identifiers with CGC & molecular names (when known) sequences/rna - WormBase rna gene data.
    15 KB (1,610 words) - 11:20, 21 December 2011
  • WormBase-Caltech Weekly Calls March 2021
    ** CeNGEN will provide histograms that we can put on each gene page, similar to modENCODE plots (do they provide static images or data tha * Could some data (like paper class/data) go to the Alliance directly from Caltech? Could be quicker and more e
    5 KB (777 words) - 13:18, 1 April 2021
  • PMID:26412237
    ! Gene or Protein |Embryos in which ulp-2 expression was silenced by RNAi or gene mutation—ulp-2(tv380), which we generated by the CRISPR/Cas9 system (Frie
    16 KB (1,999 words) - 18:24, 28 October 2015
  • WS224
    iii) geneIDs.WS224.gz - list of all current gene identifiers with CGC & molecular names (when known) sequences/rna - WormBase rna gene data.
    15 KB (1,583 words) - 11:13, 21 December 2011
  • Construct
    This page documents the creation of the construct class and all tools needed for its curation. ...d alleles, and expression markers used in analysis of expression patterns, gene regulation, and biological topics.
    10 KB (1,537 words) - 17:05, 28 May 2021
  • WormBase-Caltech Weekly Calls June 2016
    ...genotype; cannot always make direct, unambiguous associations to a single gene * SGD curate to gene, using controlled vocabulary
    8 KB (1,224 words) - 15:34, 21 July 2016
  • WS219
    iii) geneIDs.WS219.gz - list of all currentnt gene identifiers with CGC & molecular names (when known) sequences/rna - WormBase rna gene data.
    15 KB (1,622 words) - 11:11, 21 December 2011
  • Pipeline for identifying papers with disease or disease gene ortholog
    '''Category 1: C. elegans gene or protein''' Requirement: The gene (or protein list) needs to be kept up to date with the model organism datab
    15 KB (2,102 words) - 05:17, 25 September 2014
  • WormBase-Caltech Weekly Calls November 2015
    * May require addition of a text field tag to the ?Paper class, for example, that would capture each annotation item for a paper * Making progress towards making the graph a widget on the gene page
    6 KB (926 words) - 16:49, 3 December 2015
  • UserGuide:Revised Nomenclature
    ...i><li><i>Brugia malayi</i></ul><p>All other species in WormBase have their gene annotation imported from the authors or are predicted.</p><h2>Genomes, asse ...S and Transcript</h2><p>A CDS (coding sequence structure) is the part of a gene locus that codes for a protein product.
    56 KB (9,514 words) - 09:48, 23 October 2015
  • UserGuide:Reivsed Nomenclature
    ...i><li><i>Brugia malayi</i></ul><p>All other species in WormBase have their gene annotation imported from the authors or are predicted.</p><h2>Genomes, asse ...S and Transcript</h2><p>A CDS (coding sequence structure) is the part of a gene locus that codes for a protein product.
    56 KB (9,520 words) - 11:51, 21 October 2015
  • TAIR
    Gene Ontology Curation at TAIR 2) a standard GO Gene Association File (GAF) format
    14 KB (2,091 words) - 16:28, 9 December 2010
  • WS231
    ...G_SPECIES.WS231.geneIDs.txtgz - list of all current gene identifiers with CGC & molecular names (when known) - G_SPECIES.WS231.SRA_gene_expression.tar.gz - Tables of gene expression values computed from SRA RNASeq data
    16 KB (1,820 words) - 14:15, 13 September 2012
  • WormBase
    Gene Product in Blue '''4)''' Link out gene products IDs to MODs and UniProtKB
    11 KB (1,666 words) - 17:53, 19 June 2014
  • RNAi
    ...loss-of-function mutation in that gene, hence providing evidence as to the gene's biological function. ...s with multiple mutations in the strain receiving the dsRNA, multiple RNAi gene targets, complex genetic interactions, and/or missing descriptions from the
    29 KB (4,152 words) - 20:29, 30 July 2019
  • WormBase-Caltech Weekly Calls April 2012
    *GeneWiki for human gene annotation **One page for each gene; already have ~10,000 articles
    7 KB (1,158 words) - 17:20, 3 May 2012
  • Gene Interaction
    ...ne_regulation objects, ?YH objects, and ?Interaction objects into a single class, ?Interaction. The proposed ?Physical_interaction model has also been conso ...XREF Interaction #Interactor_info // PCR_product of the interacting gene or protein, e.g. Yeast Two Hybrid experiments
    53 KB (6,521 words) - 20:51, 7 March 2019
  • Administration:Installing WormMine
    * Generates generic per-class XML dumps for each species in <code>model</code>. ...ck the start and end of each file to ensure that the dump process for each class completed successfully.
    25 KB (3,652 words) - 23:06, 25 December 2014
  • Ontology Annotator
    *Gene class *Gene ontology
    20 KB (3,124 words) - 19:59, 19 February 2020

View (previous 250 | next 250) (20 | 50 | 100 | 250 | 500)

Retrieved from "https://wiki.wormbase.org/index.php/Special:Search"