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- | 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
