Search results
Jump to navigation
Jump to search
Page title matches
- *[[Taxon Main Page|Summary page for taxon data work]] ...367 bytes (61 words) - 09:29, 16 December 2008
- ''Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology deve [[Taxon Trigger File Metrics]] ...1 KB (201 words) - 12:08, 29 September 2011
- ...flow being used in creating or editing links between GO terms and the NCBI taxon slim. go/scratch/go-taxon/ncbitax-slim.obo ...7 KB (1,010 words) - 05:22, 1 June 2009
- [[Category:Taxon]] What is the relationship between an annotation and the taxon id assigned to that annotation? ...5 KB (860 words) - 18:40, 15 July 2014
- ...oacademy.github.io/obook/explanation/taxon-constraints-explainer/ Guide to Taxon restrictions] *Taxon restrictions are managed outside of the main ontology file, in tab-separate ...7 KB (1,136 words) - 12:00, 27 November 2023
- #REDIRECT [[Adding Taxon Restrictions]] ...39 bytes (4 words) - 21:13, 7 June 2018
- ==Taxon in GO - 27th April 2007== ...senting a way in which GO could capture relationships between GO terms and taxon. We called this meeting to discuss whether this or a modified form should b ...10 KB (1,726 words) - 18:37, 14 June 2008
- #REDIRECT [[Taxon Constraint Check Engine]] ...43 bytes (5 words) - 18:34, 17 August 2010
- [[Category:Taxon]] ...cificity so we also get all GO terms with cross products to these terms: [[Taxon-GO_Implementation_April_2008_onwards#Cross_Product_files]] ...495 bytes (75 words) - 18:49, 15 July 2014
- [[Category:Ontology]] [[Category:Taxon]] ...400 bytes (57 words) - 12:32, 14 July 2014
- [[Category:Taxon]] I am planning to move the taxon check files in cvs from ...1 KB (225 words) - 18:41, 15 July 2014
- ...2008 Jennifer presented a proposal and pilot on the system of implementing taxon information. At the Salt Lake City Meeting it was decided to implement the In starting to implement the links I am using the custom taxon slim that Chris Mungall made from the NCBI taxonomy hierarchy. ...27 KB (4,179 words) - 08:54, 11 November 2008
- Two entire taxa had gone missing from the taxon slim, and we had also lost a union_of term from the UnionTerms file. I do n Looked through the rest of Michelle's taxon spreadsheet and sent a few questions to her before doing the final edits: ...16 KB (2,543 words) - 09:19, 28 August 2009
- [[Category:Taxon]] go/scratch/go-taxon/ncbitax-slim.obo ...1 KB (239 words) - 18:40, 15 July 2014
- ...pt has produced. It is called gaf-taxon-gaffes.txt and is in go/scratch/go-taxon. TAXON RULE INCORRECT. (DEF OF GO TERM INCLUDES CYANOBACTERIUM) GO:0030089 "phyco ...28 KB (3,620 words) - 10:49, 4 September 2009
- [[Category:Taxon]] ...to change the pipeline and so it would be best for FlyBase if part of the taxon checking script protocol would be to delete these lines before the files ar ...6 KB (854 words) - 18:37, 15 July 2014
- [[Category:Taxon]] TAXON RULE INCORRECT? 1 HAMAP:MF_01631 - TAXON RULE INCORRECT? an E.coli annotation to GO:0000902 cell morphogenesis. Defi ...10 KB (1,156 words) - 18:37, 15 July 2014
- [[Category:Taxon]] ...2 KB (363 words) - 18:37, 15 July 2014
- [[Category:Taxon]] ...nore them, modify the SP keyword/interpro annotation stream or rewrite the taxon rule. I'd be interested in hearing other peoples' thoughts on this and to s ...3 KB (441 words) - 18:38, 15 July 2014
- [[Category:Taxon]] ...e better to make the ontology changes and then later come back and add the taxon rules. ...6 KB (805 words) - 18:38, 15 July 2014
- [[Category:Taxon]] ==Taxon inconsistent terms coming from electronic annotation through the InterPro2G ...8 KB (979 words) - 18:38, 15 July 2014
- [[Category:Taxon]] This was an overly tight taxon rule that has been relaxed. It was also shown up by the prokaryote subcateg ...1 KB (158 words) - 18:39, 15 July 2014
- [[Category:Taxon]] taxon checks that Jen has generated? I'm very confused ...1 KB (203 words) - 18:39, 15 July 2014
- [[Category:Taxon]] GO:0001701 in utero embryonic development only_in Theria "taxon:32525" ...2 KB (218 words) - 18:36, 15 July 2014
- [[Category:Taxon]] ...3 KB (352 words) - 18:36, 15 July 2014
- #REDIRECT [[Taxon-GO Checks and Commentary - Part 1]] ...53 bytes (7 words) - 09:37, 2 September 2009
- [[Category:Taxon]] Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope ...8 KB (1,018 words) - 18:39, 15 July 2014
Page text matches
- ''Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology deve [[Taxon Trigger File Metrics]] ...1 KB (201 words) - 12:08, 29 September 2011
- [[Category:Taxon]] I am planning to move the taxon check files in cvs from ...1 KB (225 words) - 18:41, 15 July 2014
- ==Improve Taxon constraints in PAINT== ...should take into account children and NOT just the node annotated to give taxon constraint warning ...730 bytes (106 words) - 08:59, 27 April 2020
- ===Taxon constraint family review=== ...250 bytes (35 words) - 12:54, 2 August 2021
- ==Improve Taxon constraints in PAINT== ...should take into account children and NOT just the node annotated to give taxon constraint warning ...837 bytes (133 words) - 18:16, 2 March 2020
- == Taxon Constraints == * Jim has written a plugin for Protege that will allow us to see inferred taxon constraints ...667 bytes (83 words) - 12:06, 10 August 2020
- ===Inferred Taxon constraints=== (Pascale): Is there any way to view inferred taxon constraints somewhere? See question here: https://github.com/geneontology/g ...762 bytes (92 words) - 05:13, 26 November 2018
- [[Category:Taxon]] GO:0001701 in utero embryonic development only_in Theria "taxon:32525" ...2 KB (218 words) - 18:36, 15 July 2014
- ===Taxon Constraints and Obsoletions=== ...e removed from the import file and we need to run docker to regenerate the taxon constraint file. ...941 bytes (141 words) - 09:53, 1 July 2019
- ==Update on Taxon constraints== * '''ACTION''': Dustin to check with Jim on where are the 'full' taxon constraints are, so that we use the same. ...1 KB (164 words) - 12:48, 7 July 2020
- == Taxon Constraints == *Once edited, the taxon constraints will need to be added by regenerating the imported file. ...1 KB (200 words) - 13:09, 22 October 2018
- [[Category:Taxon]] go/scratch/go-taxon/ncbitax-slim.obo ...1 KB (239 words) - 18:40, 15 July 2014
- #REDIRECT [[Adding Taxon Restrictions]] ...39 bytes (4 words) - 21:13, 7 June 2018
- ==Implementing the taxon checks== ...812 bytes (124 words) - 12:33, 27 April 2020
- #REDIRECT [[Taxon-GO Proposal 2007]] ...36 bytes (3 words) - 18:36, 14 June 2008
- #REDIRECT [[Taxon Constraint Check Engine]] ...43 bytes (5 words) - 18:34, 17 August 2010
- ==Taxon constraints== ...946 bytes (137 words) - 13:02, 4 August 2021
- ===S. japonicus taxon issue=== ...unlock 402676]. The ticket is asking whether PAINT can support the species taxon ID. ...3 KB (443 words) - 15:19, 20 September 2023
- *[[Taxon Main Page|Summary page for taxon data work]] ...367 bytes (61 words) - 09:29, 16 December 2008
- #REDIRECT [[Taxon-GO Implementation April 2008 onwards]] ...56 bytes (5 words) - 04:50, 30 April 2008
- #REDIRECT [[Taxon-GO Checks and Commentary - Part 1]] ...53 bytes (7 words) - 09:37, 2 September 2009
- ...tion of GO:0005773 "vacuole" specifies that it is eukaryotic only, but the taxon constraint limits it to "cellular_organisms," not eukaryotes. (SF# 3220821) **'''Curator answer: '''vacuole ; GO:0005773 inherits the 'cellular organism' taxon restraint from the parent term 'cell ; GO:0005623'. We'll give it a more sp ...603 bytes (80 words) - 10:33, 12 April 2019
- * direct taxon * transitive taxon (not visible, but can be filtered) ...471 bytes (74 words) - 16:09, 23 April 2014
- ==Taxon constraints== ...ps://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-530 Taxon constraint paper] (Deegan et al. 2010) ...2 KB (281 words) - 16:23, 27 February 2024
- [[Category:Taxon]] [[Category:Ontology]] scratch/go-taxon/UnionTerms.obo?rev=1.9;content-type=text%2Fplain ...607 bytes (100 words) - 16:52, 16 July 2014
- Using the GO-taxon links, we can infer when an annotation is incorrect. * http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/go-taxon/ ...2 KB (326 words) - 13:03, 22 March 2019
- ===IMPORTANT !!! Are taxon constraints gone from the GO files we distribute? === ...1 KB (149 words) - 06:24, 3 December 2018
- <i>Candida albicans</i>, taxon:5476 <i>Dictyostelium </i>, taxon:5782 ...8 KB (1,256 words) - 10:32, 8 April 2019
- ===Change 'only in taxon' to 'in taxon'=== ...1 KB (140 words) - 14:51, 20 November 2023
- ...n used for v.14.1) RefProt README file that we use to map 5-letter code to taxon ID ASPFU->330879: ==Taxon constraints in PAINT not working?== ...2 KB (367 words) - 15:41, 7 January 2020
- === Multi-organism protein binding and interacting taxon id === * [https://github.com/geneontology/go-site/issues/2103 Allow an interacting taxon with MF protein binding?] ...2 KB (205 words) - 12:32, 16 January 2024
- == Taxon == ...1 KB (173 words) - 19:36, 10 July 2013
- [[Category:Taxon]] This was an overly tight taxon rule that has been relaxed. It was also shown up by the prokaryote subcateg ...1 KB (158 words) - 18:39, 15 July 2014
- == Jim has written a plugin for Protege that will allow us to see inferred taxon constraints == https://github.com/geneontology/protege-taxon-constraints ...617 bytes (73 words) - 02:13, 11 August 2020
- Annotations with (a) the wrong aspect for a qualifier and (b) that fail taxon constraints are currently filtered out of PAINT. ==Mismatches Reference proteomes and MOD taxon IDs== ...4 KB (604 words) - 02:30, 1 September 2020
- [[Category:Taxon]] ...cificity so we also get all GO terms with cross products to these terms: [[Taxon-GO_Implementation_April_2008_onwards#Cross_Product_files]] ...495 bytes (75 words) - 18:49, 15 July 2014
- *Does this also extend to the taxon column? Interaction between two species: taxon:6239, taxon:652611 ...3 KB (419 words) - 10:30, 16 April 2014
- ===Taxon constraints=== I need to add a couple of taxon constraints stemming from SF requests. ...2 KB (292 words) - 16:57, 21 April 2014
- ===Taxon Constraint Curation === ...ylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are in ...3 KB (455 words) - 11:52, 4 April 2024
- [[Category:Taxon]] taxon checks that Jen has generated? I'm very confused ...1 KB (203 words) - 18:39, 15 July 2014
- ...ted to mention that if a term you plan to merge has taxon constraints, the taxon constraints must be edited and regenerated before doing the merge. See [[Me ...640 bytes (92 words) - 10:29, 21 October 2019
- ** Species removed: Sulfolobus solfataricus taxon id: 273057 - probably a bug. Dustin will fix this. ==Update on Taxon constraints== ...2 KB (312 words) - 12:46, 2 June 2020
- ===Taxon constraints in PAINT=== * Taxon constraint violations in PAINT spreadsheet ...2 KB (299 words) - 12:58, 22 June 2021
- ==New taxon constraints project project== ...1 KB (176 words) - 07:54, 26 October 2021
- ===Term merges and taxon constraints=== ...ted to mention that if a term you plan to merge has taxon constraints, the taxon constraints must be edited and regenerated before doing the merge. See [[Me ...1 KB (181 words) - 13:28, 28 October 2019
- ==Computed taxon constraints== ...1 KB (176 words) - 05:16, 17 November 2023
- ** What's up with dual taxon? * Send to Ben the fix the dual taxon stuff...and list to get unit tests working. ...1 KB (183 words) - 12:14, 16 September 2008
- What do we want to present ? stats, new features (better implementation of taxon constraints), what else ? ===Taxon Error reports=== ...5 KB (799 words) - 13:13, 29 September 2020
- === Taxon Checks === owltools http://purl.obolibrary.org/obo/go/extensions/x-taxon-importer.owl --merge-imports-closure --start-server -p 9999 ...2 KB (253 words) - 10:25, 25 October 2017
- == Relation for Defining and Capturing Second Taxa in Dual Taxon Annotations == ...1 KB (144 words) - 13:03, 19 October 2020
- ...ween organisms of the same species, both taxon IDs should be the same. The taxon column of the annotation file is described in more detail in the annotation === Taxon hierarchy === ...5 KB (770 words) - 18:33, 6 March 2020
- ==Taxon constraints== #Taxon constraint file may not be perfect. ...2 KB (311 words) - 06:29, 2 June 2020
- ==Discussion notes II: TAXON RESTRICTION FILE== ...riggers file subject to? Currently, for example, it's allowing conflicting taxon restrictions: ...3 KB (459 words) - 11:05, 16 November 2011
- - New taxon checks suggested? ...310 bytes (43 words) - 16:41, 9 April 2014
- - New taxon checks suggested? ...310 bytes (43 words) - 16:42, 9 April 2014
- ...oacademy.github.io/obook/explanation/taxon-constraints-explainer/ Guide to Taxon restrictions] *Taxon restrictions are managed outside of the main ontology file, in tab-separate ...7 KB (1,136 words) - 12:00, 27 November 2023
- ...escribed in more detail in the annotation file format guide. An additional taxon ID should not be added in cases where the annotation is based on sequence o ...the ethylene-mediated signaling pathway in plants, rather than using dual taxon to annotate to regulation of ethylene mediated signaling pathway ; GO:00101 ...6 KB (941 words) - 12:05, 13 April 2019
- # Check build-go, build-go-taxon, build-go-xp-chebi for their status. The weather reports show recent builds # Click on the name of the failed build (E.g. build-go-taxon) ...3 KB (403 words) - 11:23, 12 April 2019
- === Adding taxon rules in the live ontology === ...into Parent Editor and select the right relation. What happens if it is a taxon rule that is not a large class?''' ...2 KB (426 words) - 15:56, 3 April 2014
- ==='process has causal agent' o 'in taxon' -> 'in taxon'=== ...3 KB (426 words) - 14:09, 14 December 2020
- [[Category:Taxon]] [[Category:Ontology]] 4) We need an automated means of keeping the taxon data in sync with the GO files. <br> ...5 KB (812 words) - 12:52, 23 April 2014
- ==Update on Taxon constraints== * '''ACTION''': Dustin to check with Jim on where are the 'full' taxon constraints are, so that we use the same. ...5 KB (798 words) - 14:10, 1 December 2020
- [[Category:Taxon]] What is the relationship between an annotation and the taxon id assigned to that annotation? ...5 KB (860 words) - 18:40, 15 July 2014
- ...ween organisms of the same species, both taxon IDs should be the same. The taxon column of the annotation file is described in more detail in the annotation === Taxon hierarchy === ...6 KB (860 words) - 07:34, 2 April 2009
- === Dual taxon annotations === ...te col. 16. Chris proposes post-processing the file and moving the second taxon id into c16. Would be nice to have a LEGO modeled example for this type o ...3 KB (519 words) - 15:42, 1 July 2014
- ...flow being used in creating or editing links between GO terms and the NCBI taxon slim. go/scratch/go-taxon/ncbitax-slim.obo ...7 KB (1,010 words) - 05:22, 1 June 2009
- ==Test new process to when obsoleting terms with taxon constraints== ...2 KB (296 words) - 14:16, 27 February 2023
- ==Taxon constraint== ...2 KB (285 words) - 11:25, 25 August 2021
- ==Test new process to when obsoleting terms with taxon constraints== ...2 KB (270 words) - 03:31, 8 May 2023
- ...holog. Use the strain ID in the taxon column. We currently use K12 for the taxon for E. coli, so we don't make annotations at the species level for this. Sh ...1 KB (253 words) - 09:51, 15 April 2019
- ==Consider moving taxon constraints back into ontology== ...2 KB (245 words) - 09:52, 31 January 2023
- [[Category:Ontology]] [[Category:Taxon]] ...400 bytes (57 words) - 12:32, 14 July 2014
- ==Consider moving taxon constraints back into ontology== ...2 KB (252 words) - 03:09, 10 January 2023
- ...(see [[Taxon-GO_Implementation_April_2009_onwards#5th_August_2009]] and [[Taxon-GO_Implementation_August_28th_2009_onwards]] for latest) ...3 KB (379 words) - 09:16, 2 October 2009
- === Taxon Constraints === *Proposal: keep a separate yaml file of taxon constraints ...3 KB (430 words) - 12:53, 1 October 2018
- ...aints anymore, since it was only showing 'only in taxon' and not 'never in taxon'. We will restore once the indexing issue is resolved. ...2 KB (300 words) - 12:03, 19 March 2024
- === Capturing interacting taxon === ...in the GAF (Taxon, pipe separated when more than one) or GPAD (Interacting taxon) with no relation. ...4 KB (571 words) - 12:49, 1 December 2020
- ==Uberon taxon constraints are too stringent== # Taxon constraints: ...5 KB (724 words) - 05:40, 15 August 2022
- * What's up with dual taxon? * Dual taxon ...1 KB (187 words) - 12:04, 19 August 2008
- * How is dual taxon going? * check in file, then check in DB (dual taxon, Amelia) ...1 KB (203 words) - 17:35, 8 October 2008
- ==Test new process to when obsoleting terms with taxon constraints== ...2 KB (320 words) - 01:37, 6 April 2023
- ===New taxon contraints=== ...2 KB (370 words) - 11:32, 8 September 2021
- *Proposal to standardize GAF names to include appropriate NCBI taxon ID and text string to indicate what organism(s) are included in the file ...wer case submitting group abbreviation from GO.xrf_abbs_NCBI taxon id_NCBI taxon id name.gaf.gz ...4 KB (628 words) - 13:41, 19 August 2015
- ...(see [[Taxon-GO_Implementation_April_2009_onwards#5th_August_2009]] and [[Taxon-GO_Implementation_August_28th_2009_onwards]] for latest) ...3 KB (389 words) - 10:26, 30 November 2009
- ...cluding the taxon ID and a name that matches the label associated with the taxon ID: * Keep taxon id with file name. ...4 KB (650 words) - 02:20, 9 August 2015
- [[Category:Taxon]] Line 7: TAXON RULE INCORRECT THIS TERM SHOULD INCLUDE VIRUSES GO:0019064 "viral envelope ...8 KB (1,018 words) - 18:39, 15 July 2014
- ==Discussion notes II: OBSOLETE TAXON RESTRICTIONS== * Rather than having a separate file for obsolete taxon restrictions, could we include it in taxon_go_triggers.obo, in the format ( ...3 KB (491 words) - 12:10, 30 November 2011
- ==New taxon constraints project== ...3 KB (402 words) - 11:09, 9 November 2021
- === [[Taxon Constraint Engine]] === ...2 KB (272 words) - 10:59, 11 August 2010
- ...Saccharomyces cerevisiae (Taxon ID: 4932), and Schizosaccharomyces pombe (Taxon ID: 4896). ...5 KB (726 words) - 11:16, 12 April 2019
- === Are taxon constraints functioning properly in PAINT (Karen) === * It's possible the the taxon server was down then - another reason to have touchup running regularly ...4 KB (771 words) - 15:31, 6 January 2015
- === Are taxon constraints functioning properly in PAINT (Karen) === * It's possible the the taxon server was down then - another reason to have touchup running regularly ...4 KB (640 words) - 13:28, 16 December 2014
- ...tencies in a [[GAF]] (currently using the go-taxon links - see [[:Category:Taxon]] ) ...2 KB (374 words) - 10:59, 29 April 2014
- === Capturing interacting taxon === ...in the GAF (Taxon, pipe separated when more than one) or GPAD (Interacting taxon) with no relation. ...5 KB (663 words) - 15:43, 15 December 2020
- * Addition of stable rule ids to GO taxon constraints (Emily) ...668 bytes (89 words) - 16:24, 9 April 2014
- ===FOLLOW-UP: Taxon triggers=== ...2 KB (359 words) - 19:55, 7 November 2012
- taxon_ids: ID* (only for taxon checks) === Filter by Taxon === ...7 KB (827 words) - 15:37, 14 April 2014
- * AI Pascale: Set up Taxon Constraint Summer camp with Jim, Pascale, Paul, Chris ...746 bytes (110 words) - 04:23, 31 August 2022
- ==Test new process to when obsoleting terms with taxon constraints== ...3 KB (398 words) - 04:32, 20 March 2023
- ...taxon contraints reviewed for manual annotations in the GOC, format of GO taxon constraints developed (Emily ++) | Stable rules for GO taxon constraints made available ...4 KB (534 words) - 10:26, 8 April 2019