Search results
From WormBaseWiki
Jump to navigationJump to searchCreate the page "GO term" on this wiki! See also the search results found.
Page title matches
- Term ?Text ...Version UNIQUE Text UNIQUE Text // Lincoln, to store version number of GO2 KB (183 words) - 13:25, 4 October 2010
Page text matches
- ...rsions of GO terms exist (deprecated, secondary IDs and current), eg., the term 'aging', at least two aging terms come up. (ontology file issue, both exist GO:00075681 KB (202 words) - 00:28, 25 June 2013
- *Entering a new component and GO term using free text ...erm and GO id are entered together in one column and the ID column says no GO id found1 KB (215 words) - 19:04, 11 June 2013
- Gene Ontology (GO) is a controlled vocabulary aimed at capturing three different aspects of a Gene Ontology is extensively documented at the official Web page of the GO Consortium: http://www.geneontology.org and has also been described in the2 KB (361 words) - 18:27, 17 August 2010
- ==Comments concerning GO linking of this paper== *authors discuss many types of 'aging', which are all linking to one GO term "aging"- the authors are setting out to distinguish aging events that occur3 KB (442 words) - 21:09, 1 August 2011
- ==Comments concerning GO linking of this paper== ...because the term in the text is part of a phrase that should have its own term or when linked alone does not reflect the actual meaning of the phrase it i3 KB (511 words) - 21:07, 1 August 2011
- ...s to a page that lists the index of Textpresso Cellular Component Terms to GO Cellular Component (CC) Terms. This index is organized alphabetically and ...ting on GO term names when searching from the Search page or selecting new GO terms during curation.3 KB (431 words) - 14:55, 8 July 2014
- **For the '''Second Dataset''' select '''GO Term''' as we will use this dataset to filter for serine/threonone kinases, ..., and enter <span class="Apple-style-span" style="font-weight: bold;">GO:0004674 (<span class="Apple-style-span" style="font-weight: normal;">protei2 KB (305 words) - 10:42, 31 January 2013
- The Gene Ontology (GO) project (www.geneontology.org) has a central goal of building a controlled ...Ontology project is extensively documented at the official web page of the GO consortium: http://www.geneontology.org3 KB (502 words) - 18:28, 17 August 2010
- #GO term ##Search could be on GO ID or term string.5 KB (764 words) - 21:17, 18 March 2013
- Note: only one search failed - the GO term search using string 'M band'. Everything else worked great. *GO Term911 bytes (147 words) - 20:11, 9 May 2013
- ...t a paper could have benefited from protein complexes being linked to SGD GO pages. ...ce for linking needs to be made more clear as this will drive the types of GO links made.2 KB (361 words) - 23:31, 11 January 2011
- ...nnotation] IDs of Type" checkbox, select "[Function] GO Term ID" and enter GO:0003700 in the box below (corresponds to transcription factor activity) ..."Function" and select "GO Term Info (merged)" checkbox (if you want to see GO annotations in addition to attributes selected by default, which you can ch2 KB (296 words) - 10:43, 31 January 2013
- :anatomy-term/term (6785 values, 0 evidence) :anatomy-term/evidence EMPTY7 KB (604 words) - 18:21, 11 November 2014
- There is a 'download' button inside each widget, or you could go directly to the url eg. In the long term, we will have a page that documents the API.437 bytes (73 words) - 22:41, 27 January 2011
- ==Mapping of GO OA fields to Postgres table names== *GO -- gop_goontology4 KB (759 words) - 23:35, 26 February 2017
- == GO term enrichment (TE) tool for WormBase == * I've done some groundwork on how we could implement the Panther GO TE tool for both C. elegans and the other core species. (Jane Lomax)3 KB (539 words) - 10:56, 5 June 2015
- ...tab bar and one just below it. Both boxes generate similar results and any term can be searched, such as: * GO term IDs, i.e. GO:0000012 KB (303 words) - 19:36, 13 November 2018
- ...distribution of GO terms is displayed in pie charts, one pie chart per GO term type. In the pie charts, slices that correspond to less than a threshold (c sub go_pie_charts: sub-component that renders GO Term pie charts2 KB (328 words) - 23:39, 13 August 2010
- *carrier different term from that defined by GO *ER -refers to a camera mount in the paper, not the GO term6 KB (970 words) - 19:52, 2 August 2011
- Anatomy_term "WBbt:0003955" "WBls:000000?" "GO:0000???" "GO:0000???" For instance the ALA anatomy term has 11 life stages appended in the tree view. the .ace will look like5 KB (702 words) - 12:59, 5 May 2014
- *compare ‘GO_term "GO:000nnnn”’ in the gp_annotation.ace and exp_goid in ExprOA and output: a) count and WBpaper list of papers that have matching GO annotations2 KB (344 words) - 20:49, 10 February 2017
- ...ase to describe relations between entities in the database, e.g. genes and GO terms. **Term3 KB (453 words) - 18:27, 20 September 2023
- term: all stages goid: LS:0000002 definition: All C. elegans development stages, term: embryo goid: LS:0000003 definition: The whole period of embryogenesis, fro19 KB (3,891 words) - 18:26, 17 August 2010
- ...in class, # concise descriptions, # of cloned genes, list of all GO-bp and GO-mf associated with genes in class ===Gene_class term info file===4 KB (704 words) - 18:19, 28 June 2011
- *file format - does dictyBase produce a gpi for GO? See: http://wiki.geneontology.org/index.php/Gene_Product_Data_File_Forma *GO term identifier (already available in Dump Annotation File)1 KB (205 words) - 17:10, 8 November 2012
- =Trial runs with linking GO terms in GSA papers= *only the GO lexicon from AmiGo will be used13 KB (2,118 words) - 16:51, 20 September 2011
- GO term - GO ID mappings2 KB (204 words) - 19:18, 17 November 2011
- Orthology/Homology and the GO annotations for Process, Function and Cell component. 6) #Qualifier - Additions to combine life stage with anatomy term in expression pattern annotation.3 KB (413 words) - 15:51, 18 September 2014
- === GO Alliance slim terms === * We need to update our GO slim terms for WB GO ribbons to be in sync with Alliance5 KB (759 words) - 15:02, 11 September 2019
- ?SO_term Term ?Text Version SOFA_ontology UNIQUE Float // Analogous to GO, the SO version number is only to be attached1 KB (117 words) - 09:34, 5 October 2010
- *Output file: go.ace **Script on tazendra: /home/acedb/kimberly/citace_upload/go/ontology2ace/go_obo2ace/go_obo_to_go_ace.pl15 KB (1,936 words) - 16:29, 29 June 2018
- ...h term, click on the "Remove" button to the right of the particular search term. Clicking on it will bring you new results. ...ase check WormBase Advanced Search for instructions on how to use AQL. Or, go to http://www.acedb.org/Software/whelp/AQL/.2 KB (315 words) - 18:27, 17 August 2010
- The new pipeline for uploading manual GO annotations will be different in that we will now get our manual annotation ...l and InterPro2GO GAF (see below) and the combined file is uploaded to the GO repository.3 KB (495 words) - 15:15, 24 August 2012
- == GO-CAM model/pathway curation with orthology data == - GO term data will address this issue2 KB (303 words) - 18:23, 16 April 2020
- Back to [[GO entity markup]] | align="center" style="background:#f0f0f0;"|'''Linked Term in Abstract'''29 KB (4,227 words) - 18:16, 21 September 2011
- GO Term Enrichment: This table shows terms from the gene ontology that are signific ...nome column has the number of genes in the entire genome annotated to that term.6 KB (964 words) - 18:49, 22 May 2018
- ...gory terms and their mapping, based on previous curation, to a GO term and GO ID. ...an autocomplete to add GO terms which should avoid any future errors in GO term entry.11 KB (1,765 words) - 15:10, 18 February 2014
- In the acedb user account on Tazendra at:/home/acedb/ranjana/GO: #copy the right go.go.<date> file from /home/acedb/ranjana/citace_upload/go_curation/go_dumper_fi4 KB (629 words) - 18:27, 23 November 2020
- -- Simplify info representation; focus on term less the method -- Action Items: Look into GO details page for ideas for rendering table; See SGDs3 KB (423 words) - 18:20, 14 February 2011
- ...lack list and filtering based upon papers already annotated with Component term in gaf file **Organization of categories by task? e.g. GO curation, Phenotype curation, Expression patterns, etc.6 KB (901 words) - 19:21, 29 November 2011
- ...ype2GO-based GO annotations will be handled for future WormBase builds and GO uploads. *If the perturbation is an RNAi experiment, we will only associate the GO annotations with phenotypes resulting from disruption of the primary target7 KB (1,164 words) - 17:54, 19 February 2015
- ...staff can take vacations. They can also help develop new web tools. Short term goal: get low hanging fruits first (SPELL, ModSEEK ...) ...l give a talk about Textpresso central and mining, also have a workshop on GO curation and LEGO.2 KB (339 words) - 18:43, 8 April 2016
- ** Term * We'll only include the Term entries6 KB (834 words) - 17:56, 15 June 2020
- 1. Go to the main page, either by entering its URL http://wormbase.org, or by cli ...any). If a single data record is found, the search routine will sometimes go directly to the Web page for that record (it will automatically do this for3 KB (545 words) - 19:56, 11 August 2010
- ...ene Ontology consortium to specify how gene associations to Gene Ontology (GO) terms would be reported in a tab-delimited download file. http://geneontology.org/docs/go-annotation-file-gaf-format-2.0/12 KB (1,718 words) - 17:45, 5 February 2021
- Term ?Text ...Version UNIQUE Text UNIQUE Text // Lincoln, to store version number of GO2 KB (183 words) - 13:25, 4 October 2010
- * Will go ahead and send emails for only new set of papers (won't resend requests for * Maybe go back to papers that already had a request sent at the 6 month time point5 KB (818 words) - 15:55, 1 November 2018
- 1) Remove the Term tag. The name of the GO_term would be populated in the 2) Add an Alt_id tag to populate secondary IDs as listed in the GO obo3 KB (433 words) - 08:32, 22 June 2015
- ...geal pumping phenotypes that were measured by EPGs be annotated with this term? These questions highlight a need to revisit the pharyngeal phenotype bran ...any other person interested in the group to help with pharyngeal phenotype term organization7 KB (1,073 words) - 16:26, 2 March 2017
- ** Phenotype, anatomy ontologies, GO, etc. === Anatomy term acronyms ===3 KB (427 words) - 15:32, 1 August 2019
- *GO Term [http://mangolassi.caltech.edu/~azurebrd/cgi-bin/testing/amigo/wobr/amigo.c **Main term and children, with annotation numbers (inferred, term and descendant annotations)5 KB (850 words) - 15:32, 5 September 2013
- ...get done in the next 1.5 years (detailed), but include some info of longer term plans and challenges we think we will face. This sketch needs vision of the ...l processes involved in, and cellular localization based on Gene Ontology (GO data)4 KB (574 words) - 01:54, 2 March 2018
- https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md ...he GPAD2.0 file, but no action needed as we don't have any negation in our GO OA annotations. || n/a10 KB (1,456 words) - 17:43, 9 November 2023
- ! GO Annotation |'''MF - GO:0016929 SUMO-specific protease activity16 KB (1,999 words) - 18:24, 28 October 2015
- * Based on 3 GO categories and homology * Add tissue-specific expression, and go live4 KB (622 words) - 16:47, 6 August 2014
- 2) sentences from papers already curated by TAIR for GO Cellular Component 3) sentences from papers not curated by TAIR for GO Cellular Component14 KB (2,091 words) - 16:28, 9 December 2010
- Do you want the name of the genes for the Tier IIs, so you can add your GO-terms, etc? == UPR GO Terms & Associated Genes ==10 KB (1,194 words) - 16:35, 13 December 2013
- * Added link in WBPerson term info to Person page with publications showing ** Not sure we came to an agreement; will go ahead with trying this6 KB (982 words) - 15:33, 2 July 2015
- *Not caught up on RNAi and allele curation by end of this term *Logical extensions to GO (we will discuss next week)6 KB (944 words) - 16:25, 1 November 2012
- ...Neurobrowse URL]. Alternatively, Neurobrowse is linked on specific Anatomy Term pages in WormBase. ..." box, at the upper left corner of the NBrowse window, and click the green GO button. For example, one queries for R2AR, a neuron in the male sensory ray2 KB (256 words) - 22:25, 5 August 2019
- ...notype2GO Annotation !! Evidence Code !! Experiment !! Reference !! Manual GO Annotation !! Evidence Code !! Comment !! Recommend Keep Phenotype2GO Annot | hsf-1 || locomotion (GO:0040011) || IMP || RNAi in rrf-3 || 6395, Simmer et al., 2003, others || No5 KB (825 words) - 21:25, 24 June 2013
- ...e follow that defined by [http://geneontology.org/docs/ontology-relations/ GO Relations] where "is a", "part of", and "regulates" are included in inferen 6. Graph display may be faceted by evidence types or ontology aspects (GO only).3 KB (506 words) - 21:32, 30 October 2019
- ''Cellular_component'' -- For linking to a GO term3 KB (320 words) - 10:55, 10 December 2010
- A general summary of the process term. Can be extracted from WormBook if possible. * Mined from GO20 KB (3,088 words) - 19:17, 13 August 2020
- * Still discussing how to handle plasmids/vectors, whether they should go in the ?Clone class (there is precedence) * We will go ahead with considering including all plasmids and vectors (e.g. AddGene & F8 KB (1,218 words) - 17:46, 2 April 2014
- =Different Types of GO Annotations= GO_term "GO:0007191" "IDA" Paper_evidence "WBPaper00006389"17 KB (2,104 words) - 22:44, 17 December 2014
- *GO recently established link outs from PubMed to AmiGO *** gene ontology (go-slim ribbons)4 KB (544 words) - 16:22, 5 January 2017
- ?SO_term Term ?Text Version SOFA_ontology UNIQUE Float // Analogous to GO, the SO version number is only to be attached3 KB (368 words) - 10:15, 1 February 2012
- ...and download the annotations in either a simple three-column format or the GO's gene_association file (GAF) format. ...ow and manually (by me) for the macromolecular interactions. For the long term, having the option to combine the SVMs with both Textpresso searches and wi17 KB (2,749 words) - 20:04, 21 January 2011
- ...o part of the broader plan for Textpresso-based curation pipelines and the GO's Common Annotation Framework. *Categories - gene/protein name, CCC, assay term, verb30 KB (4,868 words) - 14:50, 11 June 2013
- * SObA for GO will be broken until we install our own local server (Raymond working on) * Use of GO server; hasn't been reliable7 KB (1,010 words) - 17:08, 4 May 2017
- ...gene and paper have been connected to the process through other tags, i.e. GO mappings, phenotype mappings, microarray, anatomy. <br> * Associated_with -> Mappings to terms in GO and Phenotype classes <br>4 KB (503 words) - 00:51, 7 November 2013
- # I currently have XREFs between tags in the ?RO_term class and the ?GO _annotation class. Will we eventually want XREFs between all classes that ...ions eventually found their way into RO or were subsumed by an existing RO term, but I don't have a good sense right now of if and when that will happen.4 KB (691 words) - 17:16, 21 June 2018
- ...o parent term unless explicitly (and confidently) stated observed in child term/object *To pull out ncRNA genes and GO terms (Sarah Burge)4 KB (612 words) - 17:13, 1 December 2011
- *Papers can go through data tagging pipeline (SVM etc.) *Juancarlos changed obsolete anatomy terms to red text in the Term Info section of the OA6 KB (983 words) - 18:02, 12 July 2012
- * Ranjana and Valerio will go === Acquiring list of ontology term descendants ===8 KB (1,262 words) - 15:34, 3 May 2018
- Protein-to-GO Tool *If file can get to Rachel and Tony, maybe can discuss this weekend (at GO meeting)5 KB (843 words) - 17:26, 1 November 2012
- ** GO terms are not showing currently * Bypass ACEDB altogether? Go right into Datomic? Need to check, but will probably pull into ACEDB and do11 KB (1,703 words) - 15:27, 5 April 2018
- ...zation_experimental_082208. When this happens, we wanted to underline the term or phrase that was contained within both markups, but we can keep the color ...er tags within the brown (localization_cell_components_2011-02-11), so the term body would just be brown.11 KB (1,666 words) - 17:53, 19 June 2014
- * Automated descriptions to go in for WS245 ...otate a phenotype by annotating relevant DB objects, e.g. anatomy term, GO term, etc. as well as context/condition6 KB (857 words) - 16:01, 2 October 2014
- *IC annotations need GO term in With/From - DONE ...genes with an ISS and an experimental evidence code annotation to the same term14 KB (1,928 words) - 19:10, 25 January 2013
- *Link to monarchinitiative.org from WormBase? Possibly from the DO term page? there is documentation at http://monarchinitiative.org/page/services ...isease: http://monarchinitiative.org/disease/DOID_14330, from here one can go to the different tabs for Models, Genes, Compare, etc.5 KB (807 words) - 18:27, 4 September 2014
- * Who from WormBase will go? ** Raymond (SObA), Chris (Community curation), Mary Ann, Wen would like to go9 KB (1,377 words) - 16:44, 2 February 2017
- * Anatomy term example: https://wormbase.org/species/all/anatomy_term/WBbt:0005772#05--10 === Noctua/GO-CAM ===7 KB (989 words) - 16:08, 5 February 2020
- ...2010!! Number of Unique GO Terms !! % Change from 2010 !! Total Number of GO Terms !! % Change from Dec 2010 ...tion priority, contributing to ~90% of our curator efforts. Curators use a GO curation check-out form that affords curators easy visual access to the cur13 KB (1,830 words) - 16:40, 13 December 2012
- * Code developed and maintained by Joseph, but not long term solution === GO CAM/Noctua modeling ===4 KB (605 words) - 15:21, 3 March 2020
- === Phenotype term annotation summary graph === ...ppearance of label to nodes above a given size (roughly big enough to hold term name).8 KB (1,220 words) - 16:26, 3 September 2015
- 2. Select an appropriate search term. The Genome Browser requires a "Landmark or Region" (http://www.wormbase.or 3. Click the Search button and examine the results. If a search term is used that has multiple hits in the genome (e.g., zyg-*), one will get a7 KB (1,189 words) - 20:01, 11 August 2010
- '''Search''': type in an identifier or keyword and '''GO'''. ...ific GO (GeneOntology) term, genes expressed in a specific tissue (anatomy term).6 KB (1,056 words) - 21:09, 24 June 2013
- One way to go and add cell cycle specificity could be to add the ?CCO (cell cycle ontolog ...ycle ontology has XREFs to ?GO biological_process. A mapping could provide GO cc curators the info needed to fill in the Annotation_extension16 KB (1,695 words) - 08:29, 12 May 2014
- ...:Fig_1_8_07.png) Protein motifs identified by a "ribonucleoprotein" search term'''. WormBase has a extensive catalog of protein motifs, taken from both the ...lts, but also give hyperlinks to their database records, making it easy to go from a positive search result to its Gene Page or to a view of its genomic19 KB (3,061 words) - 23:01, 13 August 2010
- **How to get GO terms for a list of genes? *Problem: many genes are in intermine only as UniProt IDs from the GO Gene Association File (GAF)6 KB (864 words) - 15:32, 6 June 2013
- ...PubMed search using "Wnt" search term (not Mesh term) and C. elegans (Mesh term) ...to ask is "what are the main questions they are trying to answer when they go to the website?". When they explore a gene or protein function, what is it6 KB (974 words) - 17:28, 3 September 2014
- ! GO Term(s), IDs ...maintenance (GO:1902459), positive regulation of stem cell proliferation (GO:2000648)11 KB (1,225 words) - 19:03, 19 March 2018
- === GO annotation for Expression cluster === * Wen asking about some GO annotation details for expression clusters11 KB (1,664 words) - 16:29, 7 December 2017
- ...e data-table. This is similar to a gene being attached to more than one GO term. If a gene needs to be attached to a unrelated disease, enter all data on a Similar to: WBGene in the GO OA or concise descrips OA <br/ >14 KB (2,085 words) - 20:27, 7 July 2022
- ...wse description is visible (potential drug targets, molecular function (GO term?), secreted proteases, resistance locus, etc.)? Using radio buttons, for ex *Use GO annotations in automated fashion?9 KB (1,339 words) - 19:02, 31 January 2013
- * Papers go back to 1987, earliest paper received curation from in last week 2008 ...hook" phenotypes; correct term is "male copulatory structure variant"; the term "hook" should find "male copulatory structure"8 KB (1,189 words) - 14:10, 5 July 2018
- *Including GO terms, life stage, etc. *Need to consider how the data will be stored and referred to in the long term (via ACE files etc.)7 KB (1,117 words) - 16:39, 4 August 2011
- ...lecting a sentence for curation is quite high, since correctly assigning a GO annotation requires: ...sporter activity (even if this only leads to annotation to a high level GO term)8 KB (1,272 words) - 21:49, 19 December 2012
- | Used in human manual GO curation (Protein2GO) * What shows up in autocomplete? What shows up in term info?4 KB (572 words) - 17:01, 13 January 2021
- *Subcellular localization -> autocomplete on GO CC Can we see Wobr tree in term info? so users can navigate the tree if they need to21 KB (3,194 words) - 02:08, 17 May 2018
- *Initially thought it would be textual data that would go into disease model curation, but really involves other data types such as V * Will help Alliance project over long term3 KB (400 words) - 16:03, 15 March 2018
- ...at calls the module, the module is what generates the data, and we need to go over that if we're going to change stuff -- J''' ok ** Note: field to suggest new phenotype term. Will replace whatever term(s) are currently in the Phenotype field once it is approved23 KB (3,334 words) - 19:01, 31 October 2017
- ...raciti/oa_expr_ace_dumper/use_package.pl ||Paper<br> Gene<br> Anatomy<br> GO<br> Lifestage<br> Type<br> Transgene<br> Antibody<br> Clone<br> Strain<br> ...Gene ontology annotation|| || || || ||Kimberly Van Auken, Ranjana Kishore||GO pipeline is currently in flux as we migrate to using Protein2GO20 KB (3,050 words) - 21:01, 19 April 2017
- | :anatomy-term/evidence | :anatomy-term/reference35 KB (4,174 words) - 10:52, 2 February 2015
- [Term] id: GO:000367411 KB (1,898 words) - 16:43, 7 June 2018
- ...mean the same thing to everyone? Is there a way to assess discrepancies in term definitions among members of the community? * How do we help community curators decide the correct term?6 KB (911 words) - 17:13, 6 June 2019
- * We want some text on WOBr, GO annotation changes, automated descriptions, etc. ** We could display a notice/warning message in the form (or term info) that indicates that a paper entered in the "PubMed" field has already8 KB (1,305 words) - 23:24, 3 June 2015
- 2) sentences from papers already curated by TAIR for GO Cellular Component 3) sentences from papers not curated by TAIR for GO Cellular Component24 KB (3,814 words) - 18:31, 8 August 2011
- **In the short term we will load the Molecule CV into the Alliance (Ranjana and Michael P. will * Kimberly has occasionally uploaded a species.ace file in the context of GO curation; but Hinxton otherwise handles it; should ask them5 KB (880 words) - 15:40, 3 September 2020
- *Next GO Consortium meeting is in early November at USC ...d describe searching with general text to find matches to genes, diseases, GO terms, and orthology groups9 KB (1,490 words) - 15:35, 6 October 2016
- This obo file is used to display term info for variations, transgenes, strains, clones, rearrangements, genes in ...contains a list of terms with accompanying information for display in the term info window. This is in contrast to other flat files that only contain a s10 KB (1,644 words) - 18:48, 13 August 2020
- WS236 will go live on April 5, 2013 *Group phenotypes by e.g. anatomy term, life stage, etc.?8 KB (1,161 words) - 16:34, 7 March 2013
- ...OT||Used to indicate that the DB object is not <br/>associated with the DO term/association type||Does not exist||Qualifier||NOT ...0 or 1||NOT||Used to indicate DB object is not <br/>associated with the DO term/association type||Does not exist ||Need to add tag for WS262||WB has starte10 KB (1,599 words) - 18:53, 24 January 2019
- *GO terms *Store MySQL databases on the cloud? Bypass fire walls? Maybe for long term plan4 KB (651 words) - 16:11, 2 May 2013
- * Ontology term enrichment analysis, using ontologies other than gene ontology ** Discussed on GO call yesterday; we can/should follow up with Paul Thomas10 KB (1,464 words) - 17:09, 13 August 2015
- ...y cannot curate to individual cells, but we can annotate to a higher level term === GO curation ===12 KB (1,809 words) - 16:33, 1 March 2018
- *** What should the scope of an ontology term be? Context? Life stage? Conditions? Treatment? *** Being weary of ontology term count explosion; what's the right balance?9 KB (1,366 words) - 15:19, 6 September 2018
- 1. Term info panel (which displays info on the paper object, allele, ontology term etc.) 15. Auto update date for GO form (must be editable esp. if it's a minor edit)7 KB (1,075 words) - 21:05, 24 September 2010
- ** Ontology term enrichment aside from just Gene Ontology terms, e.g. phenotype terms ...tology annotations made to specific transcripts (not just genes; this is a GO consortium issue also)3 KB (425 words) - 13:54, 8 July 2015
- * Juancarlos has updated the GO URIs from Kimberly's suggestions; use monthly release URI or ~daily snapsho ** Should probably go with daily snapshots for curation purposes (frequent updating for new/depre5 KB (670 words) - 15:31, 3 June 2021
- <td>Go Live</td> === Go Live ===25 KB (3,632 words) - 03:11, 28 October 2013
- ...just have a browser window/tab open with topics listed, either in Process Term OA or in the Curation Status form * Example link: http://go-genkisugi.rhcloud.com/seed/model/gomodel:wb-GO_004305310 KB (1,485 words) - 18:08, 5 March 2014
- * ~9000 terms ending up as direct descendants of root term "biological process" === Reatcome/GO-CAM collaboration ===6 KB (910 words) - 15:23, 5 October 2017
- # For a given term, what is the relative number of annotations between gene 1 and gene 2. * For example, share GO SObA graph for other species13 KB (2,025 words) - 16:28, 7 November 2019
- ==GO cellular component== Curation results are stored in GO curation tables in postgres and visible in the Ontology Annotator as soon a17 KB (2,401 words) - 22:36, 29 November 2017
- * E-mails to authors for concise description and allele-phenotype will go out today/soon * Should we go to local/area meetings10 KB (1,475 words) - 16:57, 5 November 2015
- ...l curators. Information is stored in an .obo file that reports data in the Term Info box. You can also enter by typing, selecting the text finishing option This is a queryable text field. Use to clarify the assigned phenotype term.12 KB (1,991 words) - 23:45, 14 February 2011
- GO Consotrium meeting in a week and a half GO Consortium meeting this weekend7 KB (1,070 words) - 17:47, 1 March 2012
- * We want to work on/think about importing WB GO annotations into LEGO format === GO Meeting at Caltech ===8 KB (1,234 words) - 12:36, 4 June 2014
- ...tors and doing the linking on few test articles (like we are doing for GSA GO linking). --[[User:Arunr|Arunr]] 18:39, 17 August 2011 (UTC) ...synonyms probably also need the same variation processing as the original term.5 KB (857 words) - 23:28, 23 August 2011
- * If a variation needs correcting, go to /home/azurebrd/public_html/cgi-bin/data/obo_tempfile_variation !Use - OA term info8 KB (1,375 words) - 05:12, 21 April 2020
- ...directly from Wormbase and analyse its genomic context in detail. Where to go? One place to go is the Genome Browser page, which is specifically designed for just this pr6 KB (975 words) - 18:25, 17 August 2010
- |go||Gene ontology annotation||||Kimberly Van Auken, Ranjana Kishore||Gene with |process_term||Process term creation||prt_ ||Karen Yook||find WBProcess||||4 KB (580 words) - 18:13, 6 October 2017
- * Set up a time next week to go over what more needs to be done for the construct/variation/transgene class **The browser can accommodate all ontologies used by Caltech curators (all GO, Phenotype, Anatomy, Life Stage, Disease)10 KB (1,583 words) - 18:16, 5 February 2014
- Pick ‘term names’ and ‘synonyms’ from this ontology. The more term variations that the ‘master’ list has the better it will be for picking Example: The term ‘Spinal muscular Atrophy’ would have been missed because it exists in t15 KB (2,102 words) - 05:17, 25 September 2014
- ...term like IDs, synonyms etc., is displayed. The OA includes features like term autocomplete from pre-loaded ontologies, a fast AJAX loading of terms, abil *Disease Term20 KB (3,124 words) - 19:59, 19 February 2020
- *GO term stats on each class? *Gary Williams should go7 KB (1,103 words) - 18:28, 5 May 2011
- the last term generated was L4 Larva male: [Term]14 KB (2,213 words) - 19:26, 12 February 2019
- **These files will go away after a tazendra reboot ...ws_files_dir = '/home3/acedb/cron/dump_from_ws/files/'; # on tazendra to go live18 KB (2,743 words) - 17:14, 16 March 2023
- * In the short term there would be need to curate only Sequence Feature objects for these 2 exi * GO is waiting for the WB GAF to complete their September release9 KB (1,570 words) - 16:36, 21 September 2023
- ONTOLOGY DIR - gene_associations, obo files for (phenotype GO anatomy) and associated association files GO Annotation Stats WS23317 KB (2,002 words) - 14:17, 13 September 2012
- *Busy with it until had to go back to school GSA GO Linking6 KB (971 words) - 16:24, 6 October 2011
- * We could create a graph (SObA) display of topics (based on GO process) * ECO term, example: Fluorescent protein transcript localization evidence14 KB (2,226 words) - 15:31, 7 June 2018
- * Testing at juancarlos.wormbase.org (from there go to Tools > Ontology Browser) ** GO annotation10 KB (1,474 words) - 15:54, 30 April 2014
- The term "RNAi" stands for "RNA-interference" and refers to the targeted silencing o ...dence ?Variation // Explicitly record variation from which IMP manual GO annotations are made29 KB (4,152 words) - 20:29, 30 July 2019
- ...7 2027]] 'Associations' widget consistently timing out on the 'nucleus' GO Term page on Staging - '''NOT HELPDESK''' 11. TSS data will go to WS241 GBrowser. Should also be made available on FTP for download since6 KB (909 words) - 21:56, 21 November 2013
- ...ld restore tazendra up to the point when there was the security breach and go from there GSA Go-term markup5 KB (752 words) - 17:07, 7 July 2011
- * How are enzymatic pathways represented in GO, or by phenotype info? What's the cross-talk? === SObA GO on human data ===10 KB (1,527 words) - 15:32, 6 April 2017
- ...ing useful, so we increase the debug level (using -d 1) and tell it not to go into the background (using -N.) If your machine is not connected to the Int tharris> kill -TERM [PID]20 KB (2,994 words) - 16:05, 23 August 2010
- ...dd the ?Expression_annotation class and still dump anatomy, life stage and GO in the old tags. Down the line those tags will be deprecated and fully repl ?Cell and ?Cell group could go away6 KB (906 words) - 15:34, 6 December 2018
- This page documents how to go from the UniProtKB gpad file produced weekly to the WormBase .ace file for ====[[GO-CAM GPAD]]====30 KB (3,904 words) - 18:45, 13 May 2020
- ...me (2-3 business days). Since the next webinar is on Monday 9am, it should go out on Wed. or Thurs. ...he Relations Ontology class to capture the exact text string to be used in GO GAF 2.2 files (Kimberly/Michael P)5 KB (890 words) - 18:36, 5 November 2020
- | GO || Ontology terms and relationships comprising GO15 KB (2,088 words) - 16:16, 15 October 2020
- * Propose we go with Wed, Jan 16th, 1pm Pacific/4pm Eastern === Noctua / GO-CAM ===9 KB (1,364 words) - 15:39, 7 February 2019
- ...uency of GO terms in documents, and a filtering method based on high-level GO classes. The best performance of our submitted runs was 7.8% F1 and 22.2% h >35K GO terms25 KB (3,541 words) - 19:14, 11 April 2014
- <Variation> affects <Gene> function in <GO>.<br> WB WBGene00006831 unc-104 GO:0048490 WB_REF:WBPaper00045884|PMID:25329901 IMP WB:WBVar02141295 P C52E1236 KB (5,076 words) - 01:38, 2 March 2016
- '''''Cell/tissue.''' ''HSN'' (neuron) → Summary of anatomy ontology term:'' '''''Cell''' (lineage pedigree). ''Z1.ppp'' → Summary of anatomy ontology term:''14 KB (2,365 words) - 21:14, 23 July 2013
- ** GO will collaborate with Protein Ontology group to work out how to capture tha * Counting genes annotated to a term, selecting terms with 100+ annotations6 KB (906 words) - 21:38, 30 September 2015
- The following Models have been proposaed and are in a pretty good state to go in for WS250. 1) Remove the Term tag. The name of the GO_term would be populated in the9 KB (1,431 words) - 23:32, 23 June 2015
- GO Consortium meeting next week *Add "Additive" type term and "No Apparent Interaction", etc.9 KB (1,302 words) - 16:38, 2 June 2011
- ...ped, the parsing scripts look to the previous .ace file to begin assigning GO annotation ids ...le gets dumped first, and a copy put in /home/acedb/kimberly/citace_upload/go so the next script can access the final annotation number)23 KB (3,744 words) - 15:12, 23 December 2022
- Possibly introduce search links so that you can skip the gene page and go directly to the genome browser or other displays. Raymond: Is it possible to go backwards from a Wormbase modENCODE data boint to the modENCODE source?7 KB (1,182 words) - 13:50, 20 April 2012
- *AMIGO 2 might go live July 17th *** Good for visualizing "Path to Root" relationships of an ontology term7 KB (1,059 words) - 15:37, 1 August 2013
- ...record dead papers from pap_status and dead genes from gin_dead<br> paper term info will show cns_name, cns_publicname, cns_constructionsummary, cns_newtr ...ewPgid)//assigned WBConstructID||dump as Construct (Object header)<br> can term info for construct show associated transgenes?37 KB (5,333 words) - 19:07, 27 June 2019
- ***column 3 (DB_Object symbol), eg, wht-7, GO terms are from column 5. ***column 5: GOID, eg, GO:000034665 KB (9,380 words) - 22:39, 5 July 2018
- * Tool could go live for the next release * Automation still sounds like the right way to go9 KB (1,336 words) - 15:32, 2 June 2016
- ** Long term solution is implementation of ?Phenotype_experiment/?Phenotype_annotation c ...using or possibly redundant with other terms; good to get this feedback to GO7 KB (1,062 words) - 14:41, 2 August 2018
- ...Some gene model and GO term curation done(JL used EBI protein2go to do the GO curation) *** Some curation will be done this week, to go into the WS250 build11 KB (1,714 words) - 11:04, 27 July 2015
- *URL suffixes/endings will act as the RNAi.org Accession number that will go into the respective Movie objects ...sease Ontology (for eventual browsing in WOBr)? No file generated yet, but GO GAF scripts can be modified to create13 KB (1,983 words) - 16:40, 7 November 2013
- ...descendant queries for these ontologies analogous to what can be done with GO ...InterMine developers to make sure all entities associated with an ontology term can be retrieved7 KB (1,077 words) - 16:26, 20 July 2017
- * Can use GO terms, but need to be careful about how they are applied (what relationship *Long term goal would include linking to TPC and evidence sentences for validation6 KB (921 words) - 16:52, 4 January 2018
- *Would be nice to have a 'Go back to form' button from the submitted page. |(No field)||Curator history||clicking brings up term info||con_curhistory|| ||Yes12 KB (1,838 words) - 18:16, 19 May 2015
- *Do once per month: faster than currently because it doesn't have to go through the dev site *Todd: WBGene00000846, example, see how fast it loads, go from there; would like a single ACE file (concatenation of all individual a13 KB (2,097 words) - 22:48, 7 April 2011
- * When will this officially go live? * Paper-term matching powered by Textpresso6 KB (897 words) - 14:27, 3 October 2019
- | Yes - added to display of WBGene info in Term information window of OA | Yes, to make sure we don't attach GO annotations to pseudogenes.9 KB (1,464 words) - 14:10, 29 May 2015
- ...pture the evidence (eg., 'IMP', Inferred from Mutant Phenotype) on which a GO annotation is based. ...rocess, cellular component or molecular function ontology developed by the GO consortium.16 KB (2,207 words) - 23:06, 9 January 2014
- ...like to fetch the DNA sequence of (some feature or coordinates). How do I go about this? === ...y Decorated FASTA File" from the "Reports & Analysis" popupmenu. Click Go to retrieve the sequence of the region. You can also specify optional forma67 KB (10,954 words) - 09:22, 19 February 2013
- ...dra.caltech.edu/~postgres/cgi-bin/new_objects.cgi) and enter the phenotype term you want to request by clicking the “Update Phenotype!” button and fill ...example, when submitting more than one RNAi probe, as each RNAi probe must go on its own line. It is important that information that is unique to an RNAi47 KB (7,989 words) - 23:40, 1 September 2015
- ...ting as an ID but not having any data. Also, let me know where to get the Term Info for IntIDs and what to display -- J -3/28/2012 when duplicate, it will ..., I would like to do so. Autocomplete on abp_ antibody table -> name. in term information show -> original publication, location. .ace -> Antibody_info59 KB (8,367 words) - 22:00, 14 December 2018
- ...cfp, jfp. note: this data type is being assessed for SVM recognition for GO (molecular function?)<br> '''Enter new cell/anatomy term: ''' C. elegans cells or anatomy parts reported in the paper that doesn't12 KB (1,832 words) - 18:43, 11 August 2010
- 1) One way to go is to link the expression to the sequence, other than the gene. From the Ex ...rms possible cis-targets, 3. if author asserts relevant genes, that should go in some ?Regulation)24 KB (3,538 words) - 17:50, 15 December 2015
- Then on spica, login, go to the Data_for_citace/Data_from_Kimberly directory, remove the existing fi ...ts by querying for a gene, wbgene is an autocomplete (not a dropdown), the term info is populated from the gene info from the gin_ tables, not an OBO file.47 KB (6,852 words) - 04:27, 8 December 2020
- #'''Evidence Code (dis_goinference):'''Autocomplete drop-down with GO codes for now (will adopt ECO later) ===Ontology Annotator for Disease Term===36 KB (4,595 words) - 18:10, 15 March 2023
- ...he region in the paper, rather than making up our own names. I have had to go back and re-annotate regions after Xiaodong found problems with my stuff se * What time shall we meet on Monday morning and where do we go?23 KB (3,248 words) - 12:58, 22 September 2014
- |Needs to be fed to textpresso and Raymond||||Enter new cell/anatomy term||newcell||Please list any C. elegans cell or anatomy part reported in your |Needs to go to Cecilia and Textpresso||||Enter authors||authors||Please list the e-mail16 KB (2,310 words) - 11:05, 21 December 2011
- ...in WormBase already.||||We don't have a 'protein curator per se, so links go to Gene pages, we do not need to capture Protein names |Anatomy||||Enter new cell/anatomy term||newcell||Please list any C. elegans cell or anatomy part reported in your13 KB (1,960 words) - 11:07, 21 December 2011
- **go to the directory and do: ./dump_ggi_ace.pl > some_file.ace ...ioGRID is not curating protein-DNA interactions. WB has both Y1H data and GO MF data.50 KB (5,228 words) - 15:10, 21 July 2017
- '''Let's go one step further...''' * Go to /Users/danielaraciti/Desktop/Canopus/Pictures and scp the file that was120 KB (19,719 words) - 16:44, 20 October 2023
- Anatomy_term ?Anatomy_term //combines life stage with anatomy term in expr pattern annotation Life_stage ?Life_stage //combines life stage with anatomy term in expr pattern annotation104 KB (15,303 words) - 19:39, 11 May 2023
- ...r/ro.obo the ontology can be browsed here: http://www.ontobee.org/browser/term.php?o=RO&iri=http://www.w3.org/2002/07/owl%23ObjectProperty&graph=http://pu GO_term_affected: spermatid maturation (GO:0048240) RO:indirectly activates (RO:0002407)50 KB (6,966 words) - 19:15, 13 August 2020
- Long term project - PAWG continued ...rs if one is overload - This is PAWG. After done - will clear data out and go back to business.37 KB (5,533 words) - 19:17, 11 April 2014
- Long term project - PAWG continued ...rs if one is overload - This is PAWG. After done - will clear data out and go back to business.37 KB (5,533 words) - 19:17, 11 April 2014
- ...el>Temporarily solved by running server via sudo (probably not viable long term)</del> ***[http://dev.wormbase.org:8023/species/c_elegans/go_term/GO:0018996 GO:0018996] (Dev Version)29 KB (4,254 words) - 20:25, 27 April 2012
- *Sentence ID - (Ontology) sentence shows in term info; int_sentid '''Dumps as: N/A''' == To go live on tazendra ==53 KB (6,521 words) - 20:51, 7 March 2019
- 1. Go to the main page, either by entering its URL http://wormbase.org, or by cli ...any). If a single data record is found, the search routine will sometimes go directly to the Web page for that record (it will automatically do this for103 KB (16,375 words) - 23:39, 30 November 2010
- long tail - number of GO terms reasonably well predict function in 2005 777 GO terms wiht reliable redictions (ML algorithm)29 KB (4,082 words) - 19:15, 11 April 2014
- ** Will port over the WB topic and map to an ATP ontology term *** GO curation (will not port over; we can get this information from a GAF, if ne36 KB (4,994 words) - 17:27, 14 February 2024
- | align="center" style="background:#f0f0f0;"|'''Term Info''' ...rinted out in the error output file of the dumping script for a curator to go back and manually change according to best judgement.29 KB (4,575 words) - 16:23, 3 March 2022
- Term::ReadLine The first time you run this, it will go through some configuration steps. After this you will be presented with the60 KB (9,496 words) - 23:06, 13 August 2010
- ...sults for the indicated paper and datatype, or simply go the main page (or go back a page to make corrections/edits). Note that the fields for which data A link is provided to go back to the main page of the form.144 KB (18,174 words) - 19:56, 21 January 2021
- ...del helps ups capture the disease. Still challenges with holding info long term and visualizing. clinicians wnat a different view than biologists. So far, A: go yeast!31 KB (4,384 words) - 19:08, 11 April 2014
