Search results
From WormBaseWiki
Jump to navigationJump to searchCreate the page "GO term" on this wiki! See also the search results found.
- *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
