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• WormBase-Caltech Weekly Calls August 2013
  *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
• WBConfCall 2018.03.01-Agenda and Minutes
  ...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
• Noctua - Upload of WB Manual Annotations
  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/a
  10 KB (1,456 words) - 17:43, 9 November 2023
• PMID:26412237
  ! GO Annotation |'''MF - GO:0016929 SUMO-specific protease activity
  16 KB (1,999 words) - 18:24, 28 October 2015
• WormBase-Caltech Weekly Calls July 2014
  * Based on 3 GO categories and homology * Add tissue-specific expression, and go live
  4 KB (622 words) - 16:47, 6 August 2014
• TAIR
  2) sentences from papers already curated by TAIR for GO Cellular Component 3) sentences from papers not curated by TAIR for GO Cellular Component
  14 KB (2,091 words) - 16:28, 9 December 2010
• Topic Curation
  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
• WormBase-Caltech Weekly Calls June 2015
  * Added link in WBPerson term info to Person page with publications showing ** Not sure we came to an agreement; will go ahead with trying this
  6 KB (982 words) - 15:33, 2 July 2015
• WormBase-Caltech Weekly Calls July 2012
  *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
• UserGuide:Neurobrowse
  ...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 ray
  2 KB (256 words) - 22:25, 5 August 2019
• Phenotype2GO Analysis
  ...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 || No
  5 KB (825 words) - 21:25, 24 June 2013
• User Guide/SObA
  ...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
• WormBase Model:Picture
  ''Cellular_component'' -- For linking to a GO term
  3 KB (320 words) - 10:55, 10 December 2010
• Topic pages
  A general summary of the process term. Can be extracted from WormBook if possible. * Mined from GO
  20 KB (3,088 words) - 19:17, 13 August 2020
• WormBase-Caltech Weekly Calls March 2014
  * 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 & F
  8 KB (1,218 words) - 17:46, 2 April 2014
• Curation Scenarios for new GO Model - GPAD and .ace Representations
  =Different Types of GO Annotations= GO_term "GO:0007191" "IDA" Paper_evidence "WBPaper00006389"
  17 KB (2,104 words) - 22:44, 17 December 2014
• WormBase-Caltech Weekly Calls December 2016
  *GO recently established link outs from PubMed to AmiGO *** gene ontology (go-slim ribbons)
  4 KB (544 words) - 16:22, 5 January 2017
• WS230 Models.wrm
  ?SO_term Term ?Text Version SOFA_ontology UNIQUE Float // Analogous to GO, the SO version number is only to be attached
  3 KB (368 words) - 10:15, 1 February 2012
• Specifications for CCC Curation from Textpresso Search Page
  ...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 wi
  17 KB (2,749 words) - 20:04, 21 January 2011
• CCC Form 2.0 Specifications
  ...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, verb
  30 KB (4,868 words) - 14:50, 11 June 2013
• WormBase-Caltech Weekly Calls April 2017
  * SObA for GO will be broken until we install our own local server (Raymond working on) * Use of GO server; hasn't been reliable
  7 KB (1,010 words) - 17:08, 4 May 2017
• Topic (WBProcess) Model build
  ...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
• WBConfCall 2018.06.21-Agenda and Minutes
  # 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
• WormBase-Caltech Weekly Calls November 2011
  ...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
• WormBase-Caltech Weekly Calls June 2012
  *Papers can go through data tagging pipeline (SVM etc.) *Juancarlos changed obsolete anatomy terms to red text in the Term Info section of the OA
  6 KB (983 words) - 18:02, 12 July 2012
• WormBase-Caltech Weekly Calls April 2018
  * Ranjana and Valerio will go === Acquiring list of ontology term descendants ===
  8 KB (1,262 words) - 15:34, 3 May 2018
• WormBase-Caltech Weekly Calls October 2012
  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
• WormBase-Caltech Weekly Calls March 2018
  ** GO terms are not showing currently * Bypass ACEDB altogether? Go right into Datomic? Need to check, but will probably pull into ACEDB and do
  11 KB (1,703 words) - 15:27, 5 April 2018
• WormBase
  ...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
• WormBase-Caltech Weekly Calls September 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/condition
  6 KB (857 words) - 16:01, 2 October 2014
• UniProt-GOA syntax checking
  *IC annotations need GO term in With/From - DONE ...genes with an ISS and an experimental evidence code annotation to the same term
  14 KB (1,928 words) - 19:10, 25 January 2013
• WBConfCall 2014.09.03-Agenda and Minutes
  *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
• WormBase-Caltech Weekly Calls January 2017
  * Who from WormBase will go? ** Raymond (SObA), Chris (Community curation), Mary Ann, Wen would like to go
  9 KB (1,377 words) - 16:44, 2 February 2017
• WormBase-Caltech Weekly Calls January 2020
  * 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
• Progress Report 2011
  ...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 cur
  13 KB (1,830 words) - 16:40, 13 December 2012
• WormBase-Caltech Weekly Calls February 2020
  * Code developed and maintained by Joseph, but not long term solution === GO CAM/Noctua modeling ===
  4 KB (605 words) - 15:21, 3 March 2020
• WormBase-Caltech Weekly Calls August 2015
  === 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
• BASIC PROTOCOL 7: USING THE GENOME BROWSER
  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 a
  7 KB (1,189 words) - 20:01, 11 August 2010
• UserGuide:WormMine
  '''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
• Expression pattern remodel
  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_extension
  16 KB (1,695 words) - 08:29, 12 May 2014
• FIGURE(S)
  ...: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 genomic
  19 KB (3,061 words) - 23:01, 13 August 2010
• WormBase-Caltech Weekly Calls May 2013
  **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
• WormBase-Caltech Weekly Calls August 2014
  ...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 it
  6 KB (974 words) - 17:28, 3 September 2014
• Noctua model curation tracking table
  ! 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
• WormBase-Caltech Weekly Calls November 2017
  === GO annotation for Expression cluster === * Wen asking about some GO annotation details for expression clusters
  11 KB (1,664 words) - 16:29, 7 December 2017
• Old pipeline for disease data
  ...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
• WormBase-Caltech Weekly Calls December 2012
  ...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
• WormBase-Caltech Weekly Calls June 2018
  * 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
• WormBase-Caltech Weekly Calls July 2011
  *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
• Mf hmm tool
  ...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

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