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- ===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 summa4 KB (704 words) - 18:19, 28 June 2011
- Genes ?Gene XREF Gene_class648 bytes (65 words) - 12:56, 4 October 2010
Page text matches
- // ?Gene_name class to allow easier indexing of gene names and other names ?Gene_name CGC_name_for ?Gene XREF CGC_name842 bytes (93 words) - 12:59, 4 October 2010
- ...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
- |- class="datatitle" ! Class2 KB (281 words) - 21:51, 11 August 2010
- Map class Gene class3 KB (306 words) - 10:00, 26 October 2011
- == GO_annotation class == This class captures Gene::GO associateions and additional meta data associated with a curation event3 KB (337 words) - 16:15, 19 February 2015
- This Tiny class appears to have moved on from it's original remit, it is used whenever/wher ?Gene700 bytes (98 words) - 09:44, 4 October 2010
- == Display of Gene Name Evidence == * We were contacted by a user who felt our gene name evidence displayed in the Overview widget is misleading/wrong942 bytes (149 words) - 16:13, 5 May 2022
- $data{$type}{$evidence}{class} = lc($class) if(defined $class); ==use it in each class module==2 KB (265 words) - 21:11, 3 January 2012
- This cycle we see the introduction of the WBProcess class Class Addition:2 KB (207 words) - 14:11, 4 March 2011
- ...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
- 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
- // A protein structure class which will store data from the NESGC Gene ?Gene XREF 3d_data2 KB (133 words) - 09:56, 10 August 2010
- ...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
- ...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
- *Function vs Mutant Phenotype Gene Classes - Submissions to NCBI and EBI *see email thread: Function vs. mutant phenotype gene classes2 KB (329 words) - 17:10, 6 August 2015
- == Analysis class - Gary == == GO_annotation class - Kimberly ==5 KB (663 words) - 16:47, 5 December 2014
- ===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 summa4 KB (704 words) - 18:19, 28 June 2011
- ...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 gene309 bytes (39 words) - 09:49, 10 August 2010
- // WBProcess class Model - Proposed by Karen Yook WS225 // Connects to: ?Gene3 KB (275 words) - 01:07, 6 February 2014
- ...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 objects2 KB (328 words) - 23:39, 13 August 2010
- ===?Accession class retirement phase 2=== Database ?Database ?Database_field ?Accession (XREF ?Class Tag)3 KB (475 words) - 14:53, 19 February 2013
- 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
- == 5. March 1st Milestone review: Class implementation (Norie, Adrian; 15 minutes) == * Try gene as search subject1 KB (140 words) - 21:53, 16 February 2011
- // Anatomy_function class for Raymond // ?Gene and still give some information about the experiment itself.1 KB (119 words) - 10:41, 10 August 2010
- > Reflects_endogenous_expression_of ?Gene * Model change to track the Laboratory responsible for a gene class2 KB (253 words) - 14:58, 13 March 2014
- ...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 f2 KB (416 words) - 01:03, 22 July 2013
- **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
- select a, b, b->gene, e->mountain from a in class pcr_product, b in a->overlaps_cds, e in a->expr_profile->expr_map834 bytes (137 words) - 15:09, 16 June 2011
- // ?Rearrangement class // or perhaps there should be another class Complex_Rear that refers to3 KB (265 words) - 08:51, 5 October 2010
- ===?Person class=== ==?Protein Class==7 KB (881 words) - 15:46, 21 November 2013
- {| border="1" class="wikitable" |No API needed at this time; partner class of Gene and possibly Variation, Rearrangement, Locus12 KB (1,559 words) - 18:14, 15 June 2011
- === * General housekeeping - ?Accession class === ?Accession class retirement phase 18 KB (1,073 words) - 15:31, 14 December 2012
- // ?Paper class - krb 040223 // ?Paper class - krb 0402235 KB (471 words) - 16:07, 4 October 2010
- {|Class="wikitable" ! !!Acedb Tags in Annotation <br/> (From ?Disease_model_annotation class)!!Primary Object!!Number of Objects<br/>with annotations!!JSON Objects2 KB (318 words) - 17:43, 26 October 2023
- === 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
- 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, fi3 KB (575 words) - 18:47, 11 August 2010
- 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 consistenc6 KB (977 words) - 19:43, 14 June 2011
- ...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 about2 KB (358 words) - 14:03, 13 January 2014
- === 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 done1,009 bytes (150 words) - 18:13, 2 April 2013
- // ?RNAi class Inhibits Predicted_gene ?CDS XREF RNAi_result #Evidence // "gene" parent (unreliable)3 KB (312 words) - 15:14, 15 July 2010
- * '''Gene/Sequence Links''' * '''New Gene Class Name Proposal'''1 KB (165 words) - 15:47, 10 April 2015
- // ?Transcript class - krb 021126 ...fo DB_remark ?Text #Evidence // was missing from first draft of Transcript class krb4 KB (350 words) - 09:32, 17 June 2013
- 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
- *[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
- // ?Strain class Contains Gene ?Gene XREF Strain1 KB (119 words) - 16:43, 11 April 2013
- # 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
- // ?Operon class - [010928 dl] Contains_gene ?Gene XREF Contained_in_operon #Trans_splice_leader1 KB (120 words) - 09:24, 10 August 2010
- // ?Gene class - krb ?Gene Evidence #Evidence7 KB (712 words) - 10:40, 4 October 2010
- ...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 some2 KB (346 words) - 21:00, 13 November 2018
- Fetch other genes that the public name of the current gene might refer to. my $desc = 'proteins related to gene'; # skip variable assignment unless necessary9 KB (1,048 words) - 14:59, 15 February 2011
- 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
- === Genotype class === ===Genotype class===5 KB (701 words) - 15:38, 4 June 2020
- Lots of unused tags, but acedb internal class. // min, max - else min, max gene/locus2 KB (208 words) - 14:36, 4 October 2010
- ...ee 4 simple changes/additions and the re-working of the Expression_cluster class. ?Gene2 KB (199 words) - 13:31, 19 August 2011
- 1) Automated_descriptions in the ?Gene class < // Explination about class/objectcount limits3 KB (413 words) - 15:51, 18 September 2014
- ...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
- // ?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
- //Position_Matrix class Bound_by_gene_product ?Gene XREF Product_binds_matrix #Evidence //Addition by Gary Williams1 KB (125 words) - 15:01, 4 October 2012
- ...s from phenotype annotations are added to the references on the respective gene page. Gene WBGene000008985 KB (749 words) - 19:47, 17 May 2018
- // ?Expression_cluster class Gene ?Gene XREF Expression_cluster #Evidence //Igor: populated during build2 KB (177 words) - 22:50, 6 December 2010
- ...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
- // ?Microarray_results class Gene ?Gene XREF Microarray_results #Evidence // should be mapped during the bu2 KB (152 words) - 14:44, 4 October 2010
- 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 choice4 KB (568 words) - 11:06, 23 May 2011
- === 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
- ## [[UserGuide:Gene_Ontology|Gene Ontology]] ## [[UserGuide:Gene_Page|Gene Page]]3 KB (338 words) - 17:04, 6 August 2019
- ** 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
- ...readsheets.google.com/a/wormbase.org/ccc?key=tygSYCz49YW5hyCcYMHUZ1Q#gid=2 Class conversion matrix] *** Search mechanism; multi-class3 KB (378 words) - 20:23, 2 March 2011
- ...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 function5 KB (821 words) - 22:36, 20 February 2020
- === Gene association file formats on FTP === * WormBase has a ?Transcription_factor class that is currently underutilized6 KB (861 words) - 19:23, 5 November 2020
- ...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
- ...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 wa1 KB (209 words) - 19:57, 25 July 2012
- {| class="wikitable" * gene:WormBase5 KB (723 words) - 19:36, 29 August 2013
- ...proteins (Wormpep) and they are displayed in the context of the Wormbase gene page. // Found 14876 objects in this class3 KB (408 words) - 23:36, 13 August 2010
- * only gene-gene or TF-gene/feature-gene/feature-TF too? // ?Phenotype_info Class8 KB (879 words) - 09:32, 3 February 2012
- This is a huge class with many deprecated elements. // ?Sequence class12 KB (1,258 words) - 09:29, 5 October 2010
- // XREF from ?Antibody to ?CDS class will be added after ?CDS is integrated // No connection to CDS is required - just Gene is fine3 KB (318 words) - 00:53, 7 December 2010
- ===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
- *Working on concise descriptions of gene classes *Inconsistencies/discrepancies of gene class names7 KB (1,103 words) - 18:28, 5 May 2011
- * 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
- === Genotype class === ...ocument to draw up ?Genotype class and make appropriate changes to ?Strain class9 KB (1,368 words) - 15:27, 4 October 2018
- ...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
- Gene ontology: http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology *gene association10 KB (1,644 words) - 18:48, 13 August 2020
- classes/ // class-specific templates gene/ // widget templates specific for the gene class5 KB (687 words) - 14:10, 19 June 2014
- <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
- '''1) ?Person class''' '''4) ?Protein Class'''6 KB (909 words) - 21:56, 21 November 2013
- 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 bas10 KB (1,696 words) - 17:21, 25 July 2013
- 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 i2 KB (329 words) - 15:21, 7 August 2014
- * ~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
- The Categories would be gene-specific and we will supply information for: * Remove redundant gene-paper associations4 KB (556 words) - 12:45, 21 May 2019
- {| border="1" class="wikitable" ! Class16 KB (2,207 words) - 23:06, 9 January 2014
- Historical_gene ?Gene #Evidence Promoter Driven_by_gene ?Gene XREF Drives_Transgene13 KB (1,341 words) - 20:12, 22 September 2015
- ...map_positions.WS181.gz - Interpolated map positions for each coding/RNA gene xiii) geneIDs.WS181.gz - list of all current gene identifiers with CGC & molecular names (when known)8 KB (885 words) - 16:47, 21 December 2011
- // Feature class Associations Associated_with_gene ?Gene XREF Associated_feature #Evidence // richard4 KB (394 words) - 08:39, 16 September 2014
- // ?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
- ** changing the Person class to add a PI tag would be possible * Gene Classes vs Biotypes from Sequence Ontology Terms - specificity/uniqueness/p1 KB (207 words) - 09:45, 22 January 2016
- * GFF3 file issues -- names in objects; need info on the gene level (LS) * class level disambiguation1,022 bytes (140 words) - 09:36, 7 April 2011
- 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
- * 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
- ...ene.t http://bitbucket.org/tharris/wormbase/src/tip/t/WormBase/API/Object/Gene.t ok 3 - The object isa WormBase::API::Object::Gene6 KB (980 words) - 18:48, 11 August 2010
- * ?Person class - Database tag added for ORCID ...ne_cluster - Karen would like to use this underused class for phylogenetic gene clusters8 KB (1,246 words) - 15:52, 12 November 2013
