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- Archived Interaction documentation may be found [[Gene_Interaction/archive | here]] ==Interaction Curation==53 KB (6,521 words) - 20:51, 7 March 2019
- This class holds 3 types of interaction data: 1) ''Genetic Interaction''1 KB (143 words) - 21:51, 11 August 2010
- // ?Interaction class for Andrei WBInteraction00000001 // Replaces the old interaction model. The main enhancements are information about the interactors and the12 KB (1,431 words) - 19:06, 20 March 2012
- =Interaction Curation= ===upload Gary and Chris RNAi-based interaction objects into OA===50 KB (5,228 words) - 15:10, 21 July 2017
- ...Gunsalus' group at NYU. This tool is used by Wormbase to display Wormbase interaction data. ...er at this time and is installed manually. After it is installed, Wormbase interaction data needs to be dumped from AceDB and loaded to MySQL. Finally, the data i7 KB (1,133 words) - 17:52, 16 August 2010
- ...jects in Wormbase: Interaction and YH. Interaction class holds a number of interaction types (regulation, predicted, etc.). Objects in the YH class are of Y2H and ...isplay in the gene page aims to provide a consolidated compact view of the interaction objects in Wormbase. It replaces the previous views.2 KB (328 words) - 23:39, 13 August 2010
Page text matches
- ====i) ?Interaction and #Interactor_info==== ====?Interaction====321 bytes (39 words) - 13:06, 17 August 2012
- ...see 3 model change, 2 effecting the ?Variation Class and on effecting the ?Interaction class === ?Interaction ===2 KB (198 words) - 15:32, 19 September 2013
- This class holds 3 types of interaction data: 1) ''Genetic Interaction''1 KB (143 words) - 21:51, 11 August 2010
- = Agenda and Notes - BioGRID and WB interaction meeting.= ;item 1 - Mapping of Physical interaction terms/types between WB and BioGRID.1 KB (240 words) - 22:36, 22 February 2011
- ;item 1 - Interaction Display ;item 1 - Interaction Display1 KB (219 words) - 22:52, 12 January 2011
- ...jects in Wormbase: Interaction and YH. Interaction class holds a number of interaction types (regulation, predicted, etc.). Objects in the YH class are of Y2H and ...isplay in the gene page aims to provide a consolidated compact view of the interaction objects in Wormbase. It replaces the previous views.2 KB (328 words) - 23:39, 13 August 2010
- === ?Interaction model (Chris) === === ?Interaction, ?Expr_pattern, ?Antibody, ?WBProcess, and ?Construct (Chris) ===1 KB (198 words) - 17:01, 16 April 2015
- '''This cycle we see an extensive reworking of the Interaction class to allow for the better capture of Genetic interactions''' There are now 3 modules that detail the annotation of the genetic interaction.758 bytes (122 words) - 12:23, 26 July 2017
- // ?Interaction Interaction ?Interaction XREF WBProcess #Evidence2 KB (207 words) - 14:11, 4 March 2011
- ;item 2 - GO terms on interaction display109 bytes (14 words) - 22:55, 12 January 2011
- *Complicated change as needs interaction adding in lots of classes. Interaction ?Interaction3 KB (475 words) - 14:53, 19 February 2013
- [https://bitbucket.org/xdwang/ggi_oa/wiki/Home gene gene interaction OA wiki]77 bytes (13 words) - 22:51, 17 December 2010
- :: Remove interaction based phenotypes from existing tables-→ new table ;item 3 - Interaction Model (slides 4-5, attached .ppt in documents distributed section)3 KB (475 words) - 22:50, 17 December 2010
- ====='''?Interaction'''===== Interaction_phenotype ?Phenotype XREF Interaction //existing tag2 KB (260 words) - 11:11, 27 July 2012
- ...tion data]] - ''Wormbase N-Browse installation and preparation of Wormbase interaction data'' ...action Display in the Gene Page|Interaction display in the gene page]] - ''Interaction Display in the Gene Page''2 KB (293 words) - 22:32, 24 December 2010
- ==?Interaction==166 bytes (25 words) - 15:02, 5 March 2011
- // ?Interaction Interaction ?Interaction XREF WBProcess #Evidence3 KB (275 words) - 01:07, 6 February 2014
- = Agenda - BioGRID and WB interaction meeting.= ;item 2 - Mapping of interaction terms between WB and BioGRID. (Attached Excel and PowerPoint)3 KB (391 words) - 22:13, 22 February 2011
- == ?Interaction == 1) IN (Chris) I'd like to add the following tags to the main ?Interaction model: -4 KB (641 words) - 15:23, 19 June 2012
- ...nteraction datasets since both genes are involved in large scale datasets. Interaction widget is the most time consuming widget, with the most problems, which cou973 bytes (144 words) - 18:13, 6 September 2012
- === ?Interaction model changes: === ?Interaction3 KB (337 words) - 16:15, 19 February 2015
- // ?Interaction class for Andrei WBInteraction00000001 // Replaces the old interaction model. The main enhancements are information about the interactors and the12 KB (1,431 words) - 19:06, 20 March 2012
- === ?Interaction ===2 KB (227 words) - 15:59, 5 September 2013
- |gene regulation||Gene regulation||grg_||Chris Grove||Interaction with Regulatory|||| ...al<br>Interaction with Genetic<br>Interaction with Predicted<br>Paper with Interaction||||4 KB (580 words) - 18:13, 6 October 2017
- ** API/Role/Interaction.pm *** Contains the API methods needed to return the interaction data in the format needed for the Cytoscape displays1 KB (162 words) - 15:21, 28 March 2013
- Interaction ?Interaction2 KB (200 words) - 08:23, 5 October 2010
- Interaction ?Interaction XREF Molecule_interactor // Chris WS244 Interaction ?Interaction XREF Molecule_interactor // Chris WS2446 KB (543 words) - 23:29, 15 March 2016
- - subj: Addition to interaction Model (4.20) Wei wei's interaction data (emails from paul and andrei)1 KB (196 words) - 18:50, 11 August 2010
- '''ALSO''', WBPaper00004301 has Interaction objects associated with it; these should be removed is now handling the interaction data, Xiaodong? Perhaps she can correct this in the .ace file.2 KB (248 words) - 22:57, 13 August 2010
- ?Interaction Interaction_phenotype ?Phenotype XREF Interaction //existing tag4 KB (503 words) - 08:30, 22 June 2012
- Interaction model change *Triage by cases that come up for interaction or gene regulation events4 KB (695 words) - 15:26, 7 June 2012
- PPI (Protein-Protein Interaction) * Need type of interaction (physical AND proteinprotein), reference, and each gene listed4 KB (556 words) - 12:45, 21 May 2019
- * Interaction Working Group is talking about getting WormBase data into AGR * overlap between Gene Regulation / Interaction needs coordination2 KB (213 words) - 18:30, 1 February 2018
- KH - Some Caltech data seems to be missing from the WS233 upload (mostly Interaction data) KY - An interaction person will look into it.1 KB (228 words) - 16:54, 6 July 2012
- * Updates to classic interaction and interaction data compile1 KB (140 words) - 21:53, 16 February 2011
- * ?Interaction and #Interactor_info - Chris Grove ...hash and add an "Antibody_remark" field with a "?Text" entry to the main ?Interaction model.1 KB (202 words) - 12:30, 12 April 2012
- === New interaction Venn diagram tool === * Venn diagram shows how various interactors have multiple interaction types with a common focus gene4 KB (694 words) - 21:33, 19 December 2019
- '''Genetic interaction''' '''Physical interaction'''2 KB (315 words) - 03:38, 3 June 2015
- === Interaction-Gene associations === * Variations should be pushed from #Interactor_info into Interactor tag of ?Interaction model4 KB (633 words) - 19:09, 6 January 2015
- ...bsite/issues/6869 Interaction external link outs to BioGRID not working on interaction pages]2 KB (263 words) - 15:49, 4 April 2019
- ...t phenotype (IMP), Inferred from direct assay (IDA), Inferred from genetic interaction (IGI), etc. Clicking on the evidence code links to the Gene ontology consor * IGI=Inferred from Genetic Interaction3 KB (502 words) - 18:28, 17 August 2010
- ?Interaction700 bytes (98 words) - 09:44, 4 October 2010
- Physical Interaction model *Separating out from general "Interaction" model4 KB (650 words) - 17:08, 1 September 2011
- **?Interaction model "Rearrangement" tag needs an XREF and ?Rearrangement model needs an " New Interaction OA6 KB (983 words) - 18:02, 12 July 2012
- ===?Interaction and ?Feature models=== '''?Interaction model:'''7 KB (881 words) - 15:46, 21 November 2013
- Additional level of data capture within the Interaction model for Physical Interactions. ?Interaction2 KB (324 words) - 17:41, 2 June 2016
- Interaction ?Interaction3 KB (312 words) - 15:14, 15 July 2010
- * interaction network not working [https://github.com/WormBase/website/issues/8429 [#8429864 bytes (136 words) - 15:41, 21 October 2021
- Interaction dumping script *Issues of mapping interaction types: WB -> BioGRID vs. BioGRID -> WB8 KB (1,282 words) - 17:08, 7 July 2011
- ...s specific for single mutants and not phenotypes dues to interactions (see interaction phenotypes section below). ===Interaction phenotypes===7 KB (1,148 words) - 23:02, 23 October 2014
- | Interaction||Chris1 KB (200 words) - 17:59, 6 October 2017
- Textpresso Interaction Sentences *Need to discuss what sentences should be kept as adequate evidence of interaction and placed in remarks5 KB (847 words) - 17:49, 1 March 2012
- * Interaction tabs not loading https://github.com/WormBase/website/issues/6473 infrastructure - issues - needs - curation database - interaction with the db4 KB (691 words) - 17:16, 21 June 2018
- Interaction model * Interaction model still being tweaked6 KB (903 words) - 16:37, 5 January 2012
- * [[WormBase Model:Interaction|Interaction]]4 KB (568 words) - 11:06, 23 May 2011
- ...Gunsalus' group at NYU. This tool is used by Wormbase to display Wormbase interaction data. ...er at this time and is installed manually. After it is installed, Wormbase interaction data needs to be dumped from AceDB and loaded to MySQL. Finally, the data i7 KB (1,133 words) - 17:52, 16 August 2010
- Interaction ?Interaction XREF Paper Interaction ?Interaction XREF Paper10 KB (928 words) - 18:34, 2 May 2011
- * Extracting small molecule interaction data ** Any way to systematically extract small molecule interaction data? Specifically, I am looking for data about small molecules that can su3 KB (432 words) - 17:19, 18 January 2024
- ==== Unified Interaction model - Chris & Kimberly ==== ...l from the 31st of January contains the details, but basically it affects ?Interaction, and merges the ?Gene_regulation,8 KB (879 words) - 09:32, 3 February 2012
- Interaction ?Interaction XREF Paper5 KB (471 words) - 16:07, 4 October 2010
- ...ting for a genetic interaction. To distinguish these, can we include the ?Interaction ID in the With/From column along with the WBRNAi and WBPhenotype IDs? ...es assign the wrong GO term if these terms are assigned based on a genetic interaction experiment, i.e. we get the directionality wrong.7 KB (1,164 words) - 17:54, 19 February 2015
- '''11/20/09''' ACTION ITEM: Add Molecular Function binding/physical interaction categories to FlyBase implementation.904 bytes (127 words) - 18:02, 21 July 2011
- New ?Interaction model ...and speak to web team about new model before officially incorporating new ?Interaction model7 KB (1,070 words) - 17:47, 1 March 2012
- *Interaction file upload took several hours *Can objectify the Interactor_info to be a tag in the main ?Interaction model7 KB (1,019 words) - 20:58, 12 April 2012
- :interaction/interaction-summary (18885 values, 0 evidence) :wbprocess/interaction (1615 values, 0 evidence)</nowiki>7 KB (604 words) - 18:21, 11 November 2014
- ** The "Historical_gene" tag has been added to the ?Interaction, ?Transgene, ?Antibody, ?Expr_pattern, and ?WBProcess models1 KB (168 words) - 16:06, 6 June 2013
- * Need to add "Construct" under list of "Detection methods" in the ?Interaction model * Interaction OA dumper will need to be updated to accommodate constructs and transgene c4 KB (622 words) - 16:47, 6 August 2014
- === Physical Interaction Curation === * We have begun physical interaction in Interaction OA8 KB (1,120 words) - 16:19, 5 March 2015
- Interaction meeting review *Genetic interaction examples5 KB (752 words) - 17:07, 7 July 2011
- Interaction ?Interaction XREF WBProcess #Evidence4 KB (503 words) - 00:51, 7 November 2013
- * Chris: has requested a change to the Interaction model. This change is to hold new data. He will revert things for now. * Kevin: Matt is working on querying the Interaction data in Datomic. This is a difficult problem. Chris Grove offered to help i2 KB (403 words) - 16:33, 6 April 2017
- * Working with Interaction Workgroup750 bytes (89 words) - 21:57, 5 January 2011
- ...hality or behavioural responses - chemotaxis etc) or influences phenotype (interaction)1 KB (175 words) - 00:44, 27 August 2015
- * Affects ?Interaction, ?Expr_pattern, ?Antibody, ?Construct, and ?WBProcess * Gene Function & Interaction chapter almost complete7 KB (1,058 words) - 15:32, 2 April 2015
- ====How to get the unique email address for email/git interaction ====5 KB (845 words) - 17:00, 21 March 2022
- <td>Interaction</td> <td>[http://dev.wormbase.org:8023/species/c_elegans/interaction/WBInteraction0500570 WBInteraction0500570]</td>8 KB (1,190 words) - 23:28, 12 March 2012
- *WormBase predicted interaction objects can be updated simply via link to Gene Orienteer *If we want a live interaction browser, we would need to pull the data into the build process4 KB (612 words) - 17:13, 1 December 2011
- Interactor ?Interaction Interactor ?Interaction13 KB (1,341 words) - 20:12, 22 September 2015
- *Interaction model change in the works1 KB (205 words) - 16:55, 17 May 2012
- Genetic Interaction ontology Interaction object displays on WormBase website7 KB (1,158 words) - 17:20, 3 May 2012
- * cross MOD interaction1 KB (155 words) - 17:01, 19 November 2015
- *?Interaction2 KB (297 words) - 09:58, 21 May 2013
- interaction - - - -2 KB (243 words) - 20:29, 25 May 2011
- === Interaction changes === *Interaction model changed to update genetic interaction terms8 KB (1,225 words) - 16:33, 3 October 2013
- Interaction ?Interaction7 KB (712 words) - 10:40, 4 October 2010
- ...ry contains two bar-separated fields: gene name and interaction types. The interaction types are separated with semicolons.6 KB (847 words) - 23:51, 9 May 2023
- ==== Unified Interaction model - Chris & Kimberly ====5 KB (800 words) - 10:09, 17 February 2012
- === Phentoype-association file: Attributing phenotypes to genes via genetic interaction === ...otype association file currently only on direct phenotype annotations, not interaction-based phenotypes6 KB (906 words) - 21:38, 30 September 2015
- ...ome/postgres/work/citace_upload/gene_regulation/use_package.pl ||Paper<br> Interaction<br> RNAi<br> Antibody<br> Transgene<br> Variation<br> Rearrangement<br> Exp ...rove, Gary Schindelman, Kimberly Van Auken, Karen Yook|| Only one PGID per Interaction object. Some physical interactions are currently in BioGrid and will need20 KB (3,050 words) - 21:01, 19 April 2017
- *Murky genetic interaction curation? *When in doubt, curate as "genetic interaction"7 KB (1,103 words) - 18:28, 5 May 2011
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources3 KB (568 words) - 16:43, 17 February 2011
- * development for interaction display and data compile910 bytes (120 words) - 21:53, 19 January 2011
- ....bio.nyu.edu/NBrowse2/NBrowse.html N-Browse], designed for displaying gene interaction networks.2 KB (256 words) - 22:25, 5 August 2019
- =Interaction Curation= ===upload Gary and Chris RNAi-based interaction objects into OA===50 KB (5,228 words) - 15:10, 21 July 2017
- ** Ligand-receptor expression informed cell-cell interaction2 KB (247 words) - 17:22, 4 May 2023
- Physical interaction curation *On interaction OA (Tab2) physical interactions; 'Colocalizes', etc.5 KB (843 words) - 17:26, 1 November 2012
- * OA and its interaction with TC **the interaction configuration of the OA6 KB (901 words) - 19:21, 29 November 2011
- 5. [https://github.com/WormBase/website/issues/3640 3640], mig-5 interaction widget times out2 KB (277 words) - 20:30, 5 March 2015
- *Made headway on genetic interaction organization *Add "Additive" type term and "No Apparent Interaction", etc.9 KB (1,302 words) - 16:38, 2 June 2011
- * WB in best poss funding position, but lots of attention on mods, for 2 way interaction2 KB (274 words) - 15:59, 14 May 2018
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources3 KB (489 words) - 18:14, 17 August 2010
- 6. Model interaction templates to maintain consistencies.2 KB (263 words) - 19:19, 24 February 2014
- Archived Interaction documentation may be found [[Gene_Interaction/archive | here]] ==Interaction Curation==53 KB (6,521 words) - 20:51, 7 March 2019
- ...ps://github.com/WormBase/website/issues/3363 #3363] - rol-3/srf-2 Typo in ?Interaction object ** Interaction4 KB (610 words) - 13:12, 14 November 2014
- entry to the main ?Interaction model. 1a) Interaction model sign off7 KB (1,182 words) - 13:50, 20 April 2012
- ==Gene-gene interaction== ==Gene product interaction==17 KB (2,401 words) - 22:36, 29 November 2017
- ** There are many duplicates of Interaction objects in geneace, with or without two leading digits. Sometimes there is Associated_with_Interaction ?Interaction XREF Feature_interactor23 KB (3,248 words) - 12:58, 22 September 2014
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources3 KB (530 words) - 18:14, 17 August 2010
- Associated_with_Interaction ?Interaction XREF Feature_interactor4 KB (394 words) - 08:39, 16 September 2014
- ...WormBoard, CGC, Wormatlas, mirBase?, Briggsae, someone for protein protein interaction?, a pathogen person ...on by Daniela, Wen, Juancarlos). Talk also to Jae, we may want to include interaction data.5 KB (787 words) - 18:10, 25 August 2022
- * Gene interaction networks (N-browse view?) *Pathway -- pro_pathwaydb -- '''dump the same way it is dumped for Interaction''' bigtext -- until file is ready for obo_ table, ''see http://wiki.wormbas20 KB (3,088 words) - 19:17, 13 August 2020
- | :interaction/affinity-capture-ms | ?Interaction35 KB (4,174 words) - 10:52, 2 February 2015
- Changes to Interaction and Interaction_type to allow inclusion of predicted interaction data6 KB (706 words) - 10:50, 21 December 2011
- === BioGRID protein-protein interaction sharing ===7 KB (989 words) - 16:08, 5 February 2020
- 2. Suggestions on curating validated marker genes at WormBase and interaction with the wormcells-viz app2 KB (347 words) - 14:07, 2 July 2021
- ...capturing interaction data. We need to ‘suppress’(?) this data until the interaction model is up and running and then migrate it over to the new model. Curren ==Tab 4 – Genotype/ Genetic Interaction/ NBP Data Curation Fields==12 KB (1,991 words) - 23:45, 14 February 2011
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (717 words) - 18:20, 17 August 2010
- Interactor ?Interaction ==Interaction==20 KB (2,339 words) - 18:04, 23 September 2015
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (719 words) - 18:21, 17 August 2010
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (738 words) - 18:20, 17 August 2010
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (723 words) - 18:21, 17 August 2010
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (723 words) - 18:21, 17 August 2010
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (725 words) - 18:20, 17 August 2010
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (725 words) - 18:21, 17 August 2010
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (610 words) - 18:20, 17 August 2010
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (735 words) - 18:22, 17 August 2010
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (735 words) - 18:22, 17 August 2010
- Physical interaction model Genetic Interaction Curation7 KB (1,064 words) - 19:12, 3 November 2011
- *Interaction and Gene_regulation OA dumpers working OK *Can follow documentation on Interaction [http://wiki.wormbase.org/index.php/Gene_Interaction#Handling_Dead_Genes_Du6 KB (864 words) - 15:32, 6 June 2013
- ...ilencer' Feature has also been made at this location to aid expression and interaction curation and interaction curation [2013-07-23 gw3]"24 KB (3,538 words) - 17:50, 15 December 2015
- ****Complicated change as needs interaction adding in lots of classes.2 KB (383 words) - 11:59, 15 February 2013
- ** Interaction browser: what shall we use? **Xiaodong Wang - developing interaction OA; BioGRID (5-10 min)5 KB (644 words) - 22:02, 23 January 2013
- *create int_construct table for interaction : /home/postgres/work/pgpopulation/interaction/20140710_int_construct/create_datatype_tables.pl10 KB (1,537 words) - 17:05, 28 May 2021
- |Can you list interactions? <br>http://dev.wormbase.org/db/gene/interaction?list=WBGene00001188 | Compile interaction resources4 KB (762 words) - 18:20, 17 August 2010
- Interaction data 16200 (81.1%) Interaction data 941 (3.4%)16 KB (1,733 words) - 21:55, 11 May 2023
- * Interaction3 KB (423 words) - 18:20, 14 February 2011
- === Genetic Interaction Ontology (GIO) === * Juancarlos and Chris built a "genetic interaction calculator" to determine interaction types from quantitative phenotype inequalities10 KB (1,464 words) - 17:09, 13 August 2015
- ...on model to accommodate annotation of constructs used in in vitro physical interaction experiments; this is pending curation of (sufficient amounts of) the releva * Broaden scope to include all types of species-species interaction (?Interspecies_interaction class ???)8 KB (1,218 words) - 17:46, 2 April 2014
- * Will look into interaction and orthology flat files2 KB (346 words) - 21:47, 7 December 2011
- == Interaction Model as of WS231 == ...ation objects, ?YH objects, and ?Interaction objects into a single class, ?Interaction. The proposed ?Physical_interaction model has also been consolidated into t59 KB (8,367 words) - 22:00, 14 December 2018
- ...research evidence figure/table within article, WormBase data object (e.g. interaction, etc.) (high score) === Genetic Interaction Ontology ===13 KB (1,983 words) - 16:40, 7 November 2013
- Binary vs. Non-binary interaction display *Cytoscape and interaction table are only displaying interactions as binary interactions, regardless o8 KB (1,161 words) - 16:34, 7 March 2013
- ...notype ontology, perhaps we should consider moving them out to be organism interaction tags, along with other organism relationship terms such as symbiotic, mutua ...ted for every Strain-Strain (Host-Pathogen) interaction per paper that the interaction appears in, correct?15 KB (1,892 words) - 19:54, 10 February 2017
- | [[WormBase Model:Interaction|Interaction]]12 KB (1,559 words) - 18:14, 15 June 2011
- ...curation: Curator||Genes, Variations, RNAi experiments||Gene, WPO, Genetic Interaction Ontology (in progress)9 KB (1,174 words) - 18:30, 29 August 2012
- Interaction ?Interaction XREF WBProcess #Evidence ...is with predictions from diverse transcriptional coregulation and proteome interaction data sets to assign a probability for each protein for a role in a small RN15 KB (1,645 words) - 18:54, 23 January 2014
- * Would be good to have OA (e.g. Interaction OA) feed directly into LEGO/Orion/Noctua * Will still need to compare genetic interaction datasets8 KB (1,234 words) - 12:36, 4 June 2014
- Interaction data 16116 (80.7%) Interaction data 943 (3.4%)17 KB (1,841 words) - 21:54, 11 May 2023
- **interaction (Chris) **interaction (Chris)7 KB (1,077 words) - 16:26, 20 July 2017
- * Wen considering adding interaction data to SimpleMine ** Want to indicate, for a query gene, genes for which multiple interaction types have been observed11 KB (1,703 words) - 15:27, 5 April 2018
- ** May be a good tool for displaying TF-target gene interaction display (vs. Cytoscape) * We have a table of C.elegans large scale genetic and physical interaction data10 KB (1,474 words) - 15:54, 30 April 2014
- *Compile interaction resources NOTE: no need to pre-compile Gene and Interaction data resources any more25 KB (3,632 words) - 03:11, 28 October 2013
- *[[Gene Interaction]]3 KB (325 words) - 17:36, 25 April 2023
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,729 words) - 14:15, 13 September 2012
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction8 KB (915 words) - 11:10, 21 December 2011
- Genetic Interaction Ontology Genetic Interaction Ontology6 KB (971 words) - 16:24, 6 October 2011
- * ?Interaction and ?Feature models - linking tags changed *This may also apply when we start sharing interaction data with BioGrid.8 KB (1,246 words) - 15:52, 12 November 2013
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction16 KB (1,820 words) - 14:15, 13 September 2012
- Genetic Interaction Ontology *Historical_gene tag will be added to several class models: ?Interaction, ?Transgene, ?Antibody, etc.7 KB (1,047 words) - 15:34, 4 April 2013
- # Feature/Interaction curation * Sequence features (?Feature objects) are now curatable as interaction entities (interactors) for physical or regulatory interactions10 KB (1,664 words) - 17:02, 4 December 2013
- Mike Cusick, from Marc Vidal's group, took interaction database curators to task for not weeding out high3 KB (564 words) - 19:15, 10 August 2010
- ...single-pass transmembrane protein, CWP-5, though the significance of this interaction for polycystic kidney disease is unknown. <br /> ...single-pass transmembrane protein, CWP-5, though the significance of this interaction for polycystic kidney disease is unknown." "Homo sapiens" Paper_evidence "W14 KB (2,085 words) - 20:27, 7 July 2022
- ...a), Gene Regulation (Xiaodong), Gene interation and overexpression of gene interaction (Chris, Gary, Karen). NOTE: interaction and protein call the "False Positive" tables 'falsepositive' instead of ob9 KB (1,321 words) - 21:59, 3 May 2020
- ...uggests organizing a heirarchy of identifiers. After the call, Chris said interaction data that comes from personal communication is not going into Alliance, and3 KB (511 words) - 18:54, 18 February 2021
- ...g), Phenotype observed (or not_observed), Gene Regulation objects, Genetic Interaction objects, species, and general remarks about the experiment. '''New Interaction'''47 KB (7,989 words) - 23:40, 1 September 2015
- ...to be incorporated (BioID, APEX, cofractionation) – perhaps as part of an interaction viewer. * The interaction browser should have a link to Cytoscape/GeneMania for deeper interrogation11 KB (1,649 words) - 16:10, 19 July 2018
- **(Chris) BioGrid- genetic interaction ontology, working with PsiMI. Will be reviewed by yeast people this week.3 KB (560 words) - 16:24, 2 August 2012
- === Physical interaction curation === * Interaction working group; we will want to incorporate miRNA/target interactions (RNA-R12 KB (1,809 words) - 16:33, 1 March 2018
- **New model, consolidating interaction types **New genetic interaction ontology with BioGrid, SGD, etc.10 KB (1,553 words) - 18:04, 7 February 2013
- ...on very weak evidence that would not be suitable for justifying the use of Interaction objects to link them. The primary example I have would be using proximity o5 KB (663 words) - 16:47, 5 December 2014
- -rwxrwxr-x 1 todd wormbase 23764 Jul 6 14:07 interaction -rwxrwxr-x 1 todd wormbase 4292 Jul 6 14:06 interaction16 KB (1,576 words) - 17:44, 16 August 2010
- * Each interaction type will likely take ~6 months, so at the end of 1.5 years we should have4 KB (574 words) - 01:54, 2 March 2018
- 3) Interaction class - Chris === Interaction ===15 KB (2,374 words) - 16:00, 17 July 2014
- ***Integrated interaction model, genetic interaction ontology *Chris would like to get Interaction numbers (how complete are we with curation)12 KB (1,878 words) - 15:55, 6 September 2012
- *** Physical interaction curation: most DBs farm out; we do our own4 KB (544 words) - 16:22, 5 January 2017
- | Interaction || AceDB interaction class15 KB (2,088 words) - 16:16, 15 October 2020
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction17 KB (2,002 words) - 14:17, 13 September 2012
- Interactor ?Interaction8 KB (853 words) - 23:50, 16 April 2014
- * Chris emailed how interaction displays are different across MODs.5 KB (732 words) - 14:46, 29 April 2016
- |'''Genetic interactions''' ||geneint||tfp, afp, cfp||postgres||postgres- interaction table||6 KB (841 words) - 08:24, 24 October 2014
- ...Gene Regulation display can take information from "Regulatory" subtypes of Interaction objects4 KB (617 words) - 17:01, 19 July 2012
- *Icons on genes indicating drug interaction, for example **Query example: Find genes that have similar expression profile and physical interaction?9 KB (1,339 words) - 19:02, 31 January 2013
- * Raymond & Chris - fixed gene interaction table dumping script4 KB (624 words) - 17:15, 4 April 2013
- *Interaction *[[Gene_Interaction|Interaction]]20 KB (3,124 words) - 19:59, 19 February 2020
- ...s ''through chromosome-wide RNAi screens, microarray analyses, and protein interaction mapping (Ge et al., 2003; Gunsalus et al., 2005). WormBase therefore annota5 KB (855 words) - 19:57, 11 August 2010
- **[http://dev.wormbase.org:8023/species/c_elegans/interaction/WBInteraction000505644#023--10 WBInteraction000505644] **Modified Interaction page API and view to account for additions and changes to schema29 KB (4,254 words) - 20:25, 27 April 2012
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,647 words) - 10:06, 22 December 2010
- *** No phenotype, interaction, GO, expression? Anything else?5 KB (821 words) - 22:36, 20 February 2020
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction14 KB (1,572 words) - 10:37, 11 November 2011
- ...species interactions that can then be associated to relevant strain-strain interaction objects of an "?Infection" class? * Some interaction objects currently refer to multiple sequence feature objects in addition to10 KB (1,485 words) - 18:08, 5 March 2014
- *Wen will take the newest expression, physical interaction, and paper class from postgres, add them to WS279 to create a "WS279.1" ver4 KB (695 words) - 14:44, 3 December 2020
- | Name|| name: || Add name as is (but see below) || suppressor/enhancer interaction phenotypic evidence6 KB (834 words) - 17:56, 15 June 2020
- ...ork with Juancarlos to sort out OA dumping scripts for Gene_regulation and Interaction OAs4 KB (651 words) - 16:11, 2 May 2013
- ...data, could we then make the association based upon the fact that there is interaction curation for that gene using the paper as evidence? This whole idea still12 KB (1,973 words) - 20:53, 16 June 2011
- name: physical interaction evidence def: "Experimental evidence that is based on characterization of an interaction between a gene product and another molecule." [ECO:MCC]30 KB (4,868 words) - 14:50, 11 June 2013
- Changes in the ?Interaction model as proposed by Andrei. Added #Interactor_info and #Interaction_info6 KB (680 words) - 10:54, 21 December 2011
- Interactor ?Interaction ...with expression patterns, overexpression gene function phenotype, genetic interaction and gene regulation experiments. Although a script was employed to find al29 KB (4,575 words) - 16:23, 3 March 2022
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction16 KB (1,674 words) - 11:38, 20 April 2011
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,610 words) - 11:20, 21 December 2011
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,653 words) - 10:13, 18 January 2013
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction17 KB (1,758 words) - 16:47, 21 December 2011
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,583 words) - 11:13, 21 December 2011
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,756 words) - 11:21, 21 December 2011
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,622 words) - 11:11, 21 December 2011
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,738 words) - 11:20, 21 December 2011
- Interactor ?Interaction ?Interaction - citace21 KB (2,888 words) - 19:58, 9 April 2021
- ** Chris will help with Interaction OA, GeneReg OA, Phenotype OA, RNAi OA5 KB (670 words) - 15:31, 3 June 2021
- * May require ?Interaction model change if anatomy, lifestage, and/or SCL to be annotated without a re5 KB (698 words) - 16:11, 3 January 2019
- '''2) ?Interaction and ?Feature models'''6 KB (909 words) - 21:56, 21 November 2013
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction16 KB (1,762 words) - 11:10, 21 December 2011
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction15 KB (1,708 words) - 10:14, 18 January 2013
- * Interaction data ...ace for the 5'UTR of ORFs, that can be used to display gene regulation and interaction (eg. transcription-factor binding sites) for genes.12 KB (1,930 words) - 17:12, 1 February 2018
- | [[WormBase Model:Interaction|Interaction]]16 KB (2,207 words) - 23:06, 9 January 2014
- * Rose from BioGRID proposed that BioGRID curate high-throughput C. elegans interaction datasets, capturing confidence scores when available, and making those anno6 KB (861 words) - 19:23, 5 November 2020
- ...------------------------------------<br><br>added confidence info to ?Interaction<br><br>fixed typo in ?Strain Phenotype_info<br><br>-============11 KB (1,614 words) - 16:52, 21 December 2011
- *** Interaction *** Interaction13 KB (2,025 words) - 16:28, 7 November 2019
- 2) ?Interaction - tag addition and tag name change < Interactor PCR_interactor ?PCR_product XREF Interaction #Interactor_info // PCR_product of the interacting gene or protein, e.g. Ye235 KB (23,325 words) - 10:33, 3 July 2014
- Checking for duplicate values in interaction (int_) or transgene (trp_) name tables or transgene synonym tables10 KB (1,650 words) - 18:12, 29 January 2024
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction17 KB (1,950 words) - 09:37, 7 February 2012
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction17 KB (1,988 words) - 11:15, 21 December 2011
- *1484 - Download table from Interaction widget - Chris6 KB (1,069 words) - 20:52, 23 July 2013
- * Physical Interaction Curation - a relatively new data type for us, discuss existing data, strate6 KB (857 words) - 16:01, 2 October 2014
- Localizome data Note: ?Interaction class update already committed8 KB (938 words) - 10:54, 21 December 2011
- ...o automated concise description files and also to add taxon IDs to BioGrid interaction file9 KB (1,464 words) - 14:10, 29 May 2015
- **Inferred from Genetic Interaction (complementation of mouse Atp7a - MGI:99400)7 KB (1,004 words) - 17:50, 13 February 2017
- IGI Inferred from Genetic Interaction IPI Inferred from Physical Interaction21 KB (2,346 words) - 11:15, 21 December 2011
- *Maybe make a database object for each C. elegans Interolog Finder interaction7 KB (1,117 words) - 16:39, 4 August 2011
- ...rking on curating sequence features to link appropriately to Expr_pattern, Interaction (regulatory), and (maybe) Transgenes7 KB (1,059 words) - 15:37, 1 August 2013
- **2) Training and user interaction7 KB (1,074 words) - 17:19, 4 October 2012
- ...ts/d/19-txXrGi-ROFuByyLnQYvWbKl3o12KZON56qto3MN6g/edit?usp=sharing list of interaction databases] for Alliance interactions working group8 KB (1,121 words) - 14:01, 15 July 2019
- ** Tool could return GO annotations, expression patterns, phenotypes, interaction-based phenotypes, etc.8 KB (1,229 words) - 15:31, 1 June 2017
- ||| Gene Interaction and Epistasis '''Genetic interactions''' [http://tazendra.caltech.edu/~post ||| Gene Product Interaction '''Gene product interactions''' [http://tazendra.caltech.edu/~postgres/cgi-21 KB (3,156 words) - 23:03, 13 August 2010
- * We can capture complex genotype phenotypes in interaction objects, but it may be vague to end users8 KB (1,224 words) - 15:34, 21 July 2016
- * This would enable us to capture certain phenotype and genetic interaction annotations9 KB (1,336 words) - 15:32, 2 June 2016
- ** May want different versions/flavors of interaction viewers8 KB (1,228 words) - 20:57, 14 July 2020
- ...term, disease_model_annotation, transgene, construct, molecule, wbprocess, interaction9 KB (1,369 words) - 22:47, 5 August 2020
- * Ranjana will email interaction curators when she needs to, in these cases9 KB (1,490 words) - 15:35, 6 October 2016
- Direct interaction between the WD40 repeat protein WDR-23 and SKN-1/Nrf inhibits binding to ta8 KB (1,220 words) - 16:26, 3 September 2015
- Interaction ?Interaction29 KB (4,152 words) - 20:29, 30 July 2019
- ...br>int_othertwotype||dropdown||Effected other type<br>Affected other type||INTERACTION tab4||-||-||-||37 KB (5,333 words) - 19:07, 27 June 2019
- *Gene Function and Interaction google docs (Chris, Gary S., Karen, Kimberly)10 KB (1,453 words) - 18:52, 4 February 2015
- ...ion_status.cgi?action=fc&field=geneproduct (flagged-done)]||''Gene product interaction'' ||geneprod||Check if your paper reports data on protein-protein, RNA-prot17 KB (2,417 words) - 11:04, 21 December 2011
- ...ch as IPI (Inferred from Physical Interaction), IGI (Inferred from Genetic Interaction), IC (Inferred from Curator), etc. ...B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002;18 Suppl 1:S233–S240. [PubMed]30 KB (3,904 words) - 18:45, 13 May 2020
- ...used for high-throughput screening analysis of the gene function, protein interaction, cellular processing, biochemical pathways, or other chemical interactions. Interaction ?Interaction XREF Molecule_regulator50 KB (6,966 words) - 19:15, 13 August 2020
- ...begin a collaboration with the BioGRID (Biological General Repository for Interaction Datasets) to add protein binding annotations (IPI evidence code) curated fo13 KB (1,830 words) - 16:40, 13 December 2012
- Q: could you not get additional info from protein-protein interaction networks? Proteins next to each other get function?13 KB (1,803 words) - 19:13, 11 April 2014
- ...on; can stick to simple binary associations for now, forgoing details like interaction type and alleles etc.11 KB (1,676 words) - 15:28, 2 May 2019
- ** Interaction Venn diagrams (in progress; Jae and Sibyl working on)14 KB (2,226 words) - 15:31, 7 June 2018
- functional interaction plugin ...scriptome, proteome or analysing results from drug screenings or synthetic interaction studies. Integration and analysis of these data in the context of ACSN help31 KB (4,384 words) - 19:08, 11 April 2014
- '''Genetic interaction with respect to Process or Pathway''' '''Physical interaction'''47 KB (6,852 words) - 04:27, 8 December 2020
