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- *[[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
- ===Taxon constraint family review=== ...3 KB (432 words) - 18:07, 3 August 2021
- ==New taxon constraints project project== ...3 KB (388 words) - 14:06, 29 November 2021
- * Check if the taxon constraint is present in the [https://github.com/geneontology/go-ontology/b * Delete the taxon constraint as described in the [Adding_Taxon_Restrictions#Removing_a_taxon_ ...3 KB (390 words) - 06:08, 18 March 2024
- === Change to taxon constraint metadata flag === * GO has changed the ‘only in taxon’ relation to ‘in taxon’ ...3 KB (450 words) - 11:38, 12 March 2024
- ===Inheriting taxon rules from UBERON=== AI: Chris to turn on uberon taxon constraint import. If too many ...3 KB (545 words) - 06:54, 29 April 2016
- ==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
- ==Taxon constraints== ...3 KB (447 words) - 11:52, 18 August 2021
- ==New Taxon constraints== ...3 KB (444 words) - 12:04, 20 September 2021
- === Capturing interacting taxon === ...in the GAF (Taxon, pipe separated when more than one) or GPAD (Interacting taxon) with no relation. ...5 KB (764 words) - 12:16, 3 November 2020
- ===Additional taxon constraints=== (Pascale) Jim estimates that to integrate new taxon constraints that Paul proposes, and check if they are conflicting or redund ...3 KB (477 words) - 16:45, 22 July 2020
- === Adding GOTAX IDs to taxon relationships created in editors file === ...visible in GO browsers (QuickGO currently). We've been adding a number of taxon rules lately and it would be good if they could actually be applied :-) The ...4 KB (687 words) - 12:31, 15 May 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. ...7 KB (1,004 words) - 16:00, 3 November 2020
- ...0031410 PMID:11257124 IDA C AMOT, KIAA1071: Angiomotin IPI00163085 protein taxon:9606 20051207 UniProtKB ...532 PMID:11257124 IDA F AMOT, KIAA1071: Angiomotin IPI00163085 protein taxon:9606 20051207 UniProtKB... ...14 KB (1,873 words) - 11:30, 12 April 2019
- === Inferring Invalid Annotations from GO->Taxon links === * results: scratch/go-taxon ...3 KB (410 words) - 18:10, 14 July 2014
- ...a taxon, only found in a taxon, etc.) has led to the curation of a set of taxon-based "triggers" that will be used for annotation quality control. Addition ...4 KB (499 words) - 11:55, 20 August 2009
- ==Test new process to when obsoleting terms with taxon constraints== ...3 KB (372 words) - 12:05, 22 March 2023
- [[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
- ...axon ID (for multi-organism processes) || optional || 0 or 1 || 13 || ncbi taxon ID | 06 || Taxon || required || 1 || 13 || taxon:9606 || taxon:6239 ...4 KB (626 words) - 11:38, 12 April 2019
- biomolecule/taxon data in a manner similar to proposed on the mailing list here. to submit an additional file that would detail taxon, geneID, proteinID and any other relevant ...3 KB (379 words) - 09:06, 12 April 2019
- ==Taxon constraints changed at each PR??== ...files (specifically reasoned-pr.owl/reasoned.owl), that seem to related to taxon constraints: ...7 KB (993 words) - 13:05, 28 February 2022
- ==Test new process to when obsoleting terms with taxon constraints== ...4 KB (480 words) - 13:05, 15 May 2023
- *Taxon constraint check is still in the PAINT tool. It doesn't automatically inser ...cript that generates the IBA files relies on the TCV annotations to remove taxon constrain violation. With all TCVs turned off in the PAINT tool, the GAFs g ...2 KB (319 words) - 13:14, 5 October 2021
- === Taxon constraints === Taxon constraints can now be edited in gene_ontology_write.obo/owl. But for the ...2 KB (313 words) - 12:15, 3 July 2014
- ==Uberon taxon constraints are too stringent== ...3 KB (516 words) - 02:21, 29 June 2022
- ...ected; annotation groups have reviewed inconsistencies, and annotations or taxon rules adjusted ***Manuscript on [[Taxon_Main_Page|Taxon triggers]] in preparation, to be submitted to BMC Bioinformatics (Jen, Chri ...3 KB (430 words) - 15:01, 1 February 2010
- |Integrate Taxon checks, integrate protein domains, integrate known sites (active sites, lig ...747 bytes (90 words) - 10:51, 10 February 2023
- ...case the taxon triggers would have caught those problems. implementing the taxon triggers is on the high priority list for PAINT development. ...2 KB (389 words) - 11:15, 16 January 2018
- * go-taxon-groupings.owl ...940 bytes (135 words) - 10:29, 5 April 2019
- * taxon constraints * [https://github.com/orgs/geneontology/projects/71 New taxon constraints] ...6 KB (794 words) - 15:18, 14 February 2022
- | Taxon || style="color:red" | required || 1 || 13 | Taxon || style="color:red" | required || 1 || 13 ...5 KB (733 words) - 03:34, 13 September 2023
- For this prototype I am using the a taxon graph that I made long-hand. It is in cvs as go/scratch/Taxonomy.obo. id: taxon:3702 ...6 KB (1,013 words) - 12:30, 14 July 2014
- === Capturing interacting taxon === ...in the GAF (Taxon, pipe separated when more than one) or GPAD (Interacting taxon) with no relation. ...5 KB (841 words) - 12:18, 22 October 2020
- ===Mismatches Reference proteomes and MOD taxon IDs=== ..., where there are additional experimental GO annotations but to a distinct taxon ID. Not sure how we want to handle this. '' ...8 KB (1,161 words) - 14:21, 10 November 2020
- See also the 'taxon column: We need to record the second taxon in the schema. This is a current spot for this in gene_product, but it is w ...3 KB (398 words) - 18:10, 8 August 2010
- ...s. This project is on the back burner just now as I concentrate on getting taxon numbers for the consortium meeting. ...810 bytes (143 words) - 09:30, 15 April 2019
- **Taxon constraints improvements needed (Dustin) ...713 bytes (89 words) - 12:46, 27 April 2021
- ===Enhancing Taxon Constraints=== There are some technical issues to take care of, and making taxon constraints often leads to time-consuming refactors -these ultimately impro ...5 KB (870 words) - 15:18, 27 June 2014
- Paul: taxon constraints ? ...ains annotated and sometime to the species itself. Strategy to discuss for taxon ids. ...5 KB (815 words) - 13:02, 29 July 2020
- ...; currently moving "sensu" information from synonyms to definitions (see [[Taxon-GO_Implementation_April_2009_onwards#30th_July_2009|notes]] for latest) ...4 KB (497 words) - 09:57, 3 August 2009
- ==Test new process to when obsoleting terms with taxon constraints== ...4 KB (527 words) - 13:08, 8 May 2023
- ===[https://github.com/orgs/geneontology/projects/71 New taxon constraints]=== * [https://github.com/orgs/geneontology/projects/71 New taxon constraints] ...5 KB (694 words) - 10:25, 28 March 2022
- ...s.txt file for the target ontology. For example, for the addition of a new taxon, the file can be found at https://github.com/geneontology/go-ontology/blob/ * Taxon constrains get regenerated daily. Other imports weekly. ...3 KB (441 words) - 13:34, 10 February 2020
- [[Category:Taxon]] ==Taxon inconsistent terms coming from electronic annotation through the InterPro2G ...8 KB (979 words) - 18:38, 15 July 2014
- ==== New Taxon constraints==== * '''AI set up a jamboree to complete taxon constraints'''? ...4 KB (511 words) - 12:31, 27 October 2021
- .../blob/master/metadata/rules/gorule-0000015.md gorule0000015 - Dual species taxon check] **More inclusive BP terms to check rule 15 for allowing dual taxon annotations ...2 KB (352 words) - 13:59, 26 November 2019
- * [https://github.com/orgs/geneontology/projects/71 New taxon constraints] * taxon constraints ...6 KB (784 words) - 13:17, 14 March 2022
- ** edit to add needed taxon * Taxon import incomplete see [https://github.com/geneontology/go-ontology/issues/1 ...3 KB (366 words) - 12:16, 28 April 2017
- ** taxon stuff in? ...670 bytes (100 words) - 12:38, 3 June 2008
- * Run taxon constraints checks (?) ====Taxon (column 13)==== ...6 KB (907 words) - 14:15, 2 August 2018
- *DB ID Symbol Qualifier Evidence Reference With Taxon Date Source Splice *DB ID Symbol Qualifier Evidence Reference With Taxon Date Source Splice ...5 KB (743 words) - 13:15, 30 June 2014
- ** Example report file with taxon contraint violations: [http://build.berkeleybop.org/view/GAF/job/gaf-check ...1 KB (228 words) - 16:40, 9 April 2014
- ...4|SGD:S000000118|RGD:621598 P LONM_HUMAN|LONP1|IPI00005158|PRSS15 protein taxon:9606 20100409 RefGenome ...R10046_AN13|MGI:MGI:1921392 F LONM_HUMAN|LONP1|IPI00005158|PRSS15 protein taxon:9606 20100409 RefGenome ...157 KB (17,933 words) - 11:32, 14 July 2014
- === Taxon constraints file === ...onstraints into editors file. Do we want to carry on generating a separate taxon constraints purl for legacy applications? ...7 KB (1,161 words) - 16:02, 1 July 2014
- * [https://github.com/orgs/geneontology/projects/71 New taxon constraints] ===[https://github.com/orgs/geneontology/projects/71 New taxon constraints]=== ...6 KB (754 words) - 03:56, 1 February 2022
- * (Pascale) Rules, especially taxon checks: can we have this for the July release? https://github.com/geneontol ...936 bytes (130 words) - 14:19, 6 June 2018
- ===Implementation of taxon constraints=== We'd like annotations failing taxon constraints to be excluded from AmiGO and all the files we export. Can we p ...5 KB (788 words) - 17:42, 13 March 2019
- **[https://github.com/geneontology/go-ontology/issues/13269 taxon imports incomplete?] **[https://github.com/geneontology/go-ontology/issues/13343 Taxon constraint for GO:0001944] ...4 KB (647 words) - 12:58, 14 April 2017
- ...ike taxon-specific files; or we could provide a script to parse a specific taxon ...3 KB (464 words) - 11:21, 16 January 2018
- From examination of the taxon inconsistency file it would seem that these two processes are not disjoint ...e will be more terms like this. Such terms are immediately flagged up if a taxon rule is made as follows: ...5 KB (812 words) - 10:18, 10 February 2023
- === make a subset based on taxon constraints === * Requires: http://purl.obolibrary.org/obo/go/extensions/x-taxon-importer.owl ...4 KB (685 words) - 16:07, 1 July 2014
- ===[https://github.com/orgs/geneontology/projects/71 New taxon constraints]=== ...4 KB (539 words) - 01:48, 1 April 2022
- Discussion on taxon constraints ? Anything else to report ? Jim has created a plugin for Protege that allows editors to see the inferred taxon constraints. ...5 KB (899 words) - 11:56, 12 August 2020
- DB DBID Symbol Name Syn. Type Taxon WB Parent ID dx_xref WB WBGene00004804 skn-1 skn-1 gene taxon:6239 UniProtKB:P34707 ...7 KB (1,131 words) - 10:40, 9 August 2016
- ...EF:7047 RCA C Putative uncharacterized protein protein taxon:39946 20090810 GR ...RCA InterPro:IPR000209 F Putative retroelement protein taxon:39947 20090212 GR ...3 KB (468 words) - 09:47, 15 April 2019
- *DB ID Symbol Qualifier Evidence Reference With Taxon Date Source Splice *DB ID Symbol Qualifier Evidence Reference With Taxon Date Source Splice ...3 KB (401 words) - 13:14, 30 June 2014
- Release- missing 500k IBAs (taxon problems maybe??). Item 9, additional taxon constraints: Easy or not? for Jim? Seth to ping Jim<br /> ...3 KB (457 words) - 11:50, 15 July 2020
- === Taxon constraints === <pre>Taxon constraints will be easier to edit when the mega file exists, logical defs ...5 KB (854 words) - 16:02, 1 July 2014
- DB DBID Symbol Name Syn. Type Taxon WB Parent ID dx_xref WB WBGene00004804 skn-1 skn-1 gene taxon:6239 UniProtKB:P34707 ...7 KB (1,076 words) - 11:21, 27 July 2016
- How to obtain records for one taxon ID from UniProt? During the night we download all the uniprot records for the mouse taxon id. Each uniprot record has a section that lists embl and genbank records ( ...3 KB (556 words) - 17:23, 9 April 2014
- *[[Meeting Notes 4|Notes on taxon in term names]] ...1,009 bytes (121 words) - 09:50, 9 April 2019
- #* Ontology, taxon constraints: https://github.com/geneontology/go-ontology/issues ...2 KB (234 words) - 13:10, 27 February 2019
- ==New Taxon constraints== ...5 KB (688 words) - 01:48, 28 September 2021
- '''Annotations Queried as a result of taxon go trigger checks''' ...2 KB (240 words) - 11:35, 21 March 2019
- **[[Taxon_Main_Page|Taxon triggers]]: The files are now in their permanent location in cvs and most o **Manuscript on [[Taxon_Main_Page|Taxon triggers]] almost ready for submission to BMC Bioinformatics (Jen, Chris) ...3 KB (459 words) - 10:10, 16 March 2010
- * Should Taxon checks be a hard check: ...2 KB (227 words) - 09:53, 14 August 2018
- [[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
- ...WB Protein ID Symbol Name Syn. Type Taxon WB Parent ID dx_xref WB WP:CE27591 SKN-1 (?) SKN-1, isoform a ?? protein taxon:6239 WB:WBGene00004804 UniProtKB:P34707-1 ...5 KB (834 words) - 16:47, 18 July 2016
- taxon ...# GO data used; one or more of ( term def syn xref rel gp ev_code ref qual taxon ) ...3 KB (458 words) - 18:50, 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
- **[[Taxon-GO_Implementation_April_2009_onwards|Taxon triggers]] - some progress, limited by OBO-Edit filtered-save options ...3 KB (394 words) - 05:24, 1 July 2009
- **Manuscript on taxon triggers in preparation, to be submitted to BMC Bioinformatics (Jen, Chris) ***Manuscript on [[Taxon_Main_Page|Taxon triggers]] in preparation (follow links from main page for recent notes) (J ...3 KB (414 words) - 10:25, 4 January 2010
- * [http://www.geneontology.org/GO.annotation_qc.shtml#GO_AR:0000013 taxon constraints] ...m taxon violation checks is http://purl.obolibrary.org/obo/go/extensions/x-taxon-importer.owl. See [[Ontology extensions]] for more details. ...7 KB (1,049 words) - 06:38, 12 April 2019
- | taxon:10090 | taxon:10090 ...5 KB (778 words) - 18:38, 7 October 2008
- The taxon id will be provided as a definition dbxref. relationship is defined this way we will be able to choose a taxon that ...3 KB (570 words) - 17:58, 27 May 2014
- ==Taxon constraints== ...5 KB (768 words) - 09:08, 26 July 2021
- **Harold requested new taxon to be added to imports list ...1 KB (191 words) - 12:17, 7 May 2018
- ===Additional taxon constraints are now being inferred from Uberon=== ...extended characters were creating fatal errors and preventing us to commit taxon rules in OBO-Edit. ...5 KB (867 words) - 10:39, 17 November 2015
- * Taxon constraints pipeline ...1 KB (134 words) - 17:31, 7 April 2014
- ===Propagating taxon constraints from dependent ontologies=== In general, we should go for stricter taxon rules where these are implemented in e.g. UBERON where experts have given t ...6 KB (916 words) - 16:34, 10 November 2015
- **[[Taxon-GO_Implementation_April_2009_onwards|Taxon triggers]] - some progress, limited by OBO-Edit filtered-save options ...3 KB (435 words) - 12:51, 1 June 2009
- ...tion agreed; see [[Taxon-GO_Implementation_April_2008_onwards#October_22nd|taxon links]] (Jen, Chris) ...3 KB (373 words) - 07:12, 2 April 2009
- ===Inheriting taxon rules from UBERON (bumped)=== ...5 KB (749 words) - 02:41, 22 April 2016
- ...raduate student who has created taxon constraints. Regardless of where the taxon constrains come from, let’s discuss how to implement them. And to do this ...3 KB (539 words) - 12:29, 17 May 2017
- ***[[Taxon-GO_Implementation_April_2009_onwards#1st_June|Taxon triggers]] - workflow improved; implementation in progress ...3 KB (484 words) - 07:14, 10 September 2009
- ===[[Taxon_Main_Page|Taxon Triggers]]=== The taxon trigger file is a set of taxonomic restrictions for specific GO terms that ...6 KB (819 words) - 13:50, 1 July 2014
- Tentatively agreed that disjoints should and taxon constraints should go into main file, with the exception of GCI disjoints Note that reasoning with taxon constraints won't work without expansion. ...5 KB (677 words) - 16:05, 1 July 2014
- | [[Taxon Constraint Check Engine]] | [[Taxon Constraint Check Engine#v1|v1]] maintenance ...8 KB (1,037 words) - 10:52, 10 February 2023
- **Considerable progress on [[Taxon-GO_Implementation_April_2008_onwards|taxon links]], including timeline, editing pipeline, scripts, and some content (J ...3 KB (366 words) - 07:10, 2 April 2009
- ===Additional taxon constraints are now being inferred from Uberon=== ...extended characters were creating fatal errors and preventing us to commit taxon rules in OBO-Edit. ...5 KB (898 words) - 14:18, 20 November 2015
- ! Taxon | taxon:6239 ...6 KB (1,044 words) - 13:33, 18 March 2020
- ...on in PCO - I still think we need some kind of formal bridge between NCBI taxon and organism terms in CARO2/PCO. I guess this could be a simple as making ...classes that refer to protozoa altogether - or try to automate by making a taxon union class. We have since been in touch with Thomas Mock, who sent this e ...4 KB (555 words) - 16:04, 1 July 2014
- *Filtering to allow cross products and taxon link files to be filtered out: ...1 KB (243 words) - 16:22, 30 June 2014
- ...the ethylene-mediated signaling pathway in plants, rather than using dual taxon to annotate to regulation of ethylene mediated signaling pathway ; GO:00101 ...2 KB (242 words) - 18:31, 6 March 2020
- bulkloading fixed taxon updater; wasnt cleaning up directory, broke loading. ...1 KB (150 words) - 18:02, 14 July 2014
- ==== New Taxon constraints==== * '''AI set up a jamboree to complete taxon constraints'''? ...6 KB (799 words) - 11:52, 3 November 2021
- * Should Taxon checks be a hard check: ...2 KB (286 words) - 11:56, 17 August 2018
- ...d be just one part of an 'engine' of annotation QC checks - in addition to taxon there will be evidence code rules etc. We need a point person to collect an ...the files once than for all groups to merge the files and the extract the taxon they are interested in. ...6 KB (1,020 words) - 15:31, 27 June 2014
- * Species vs. strain taxon ID for ''S. pombe'' - https://github.com/geneontology/helpdesk/issues/468 ...1 KB (227 words) - 14:25, 13 February 2024
- .../go-ontology/issues/16108 GO:0071554 cell wall organization and biogenesis taxon restrictions #16108] * Should Taxon checks be a hard check: ...4 KB (586 words) - 11:49, 2 October 2018
- *[https://github.com/geneontology/minerva/issues/388 Taxon ID without label #388] ...1 KB (192 words) - 13:00, 9 February 2022
- ...classes that refer to protozoa altogether - or try to automate by making a taxon union class. We have since been in touch with Thomas Mock, who sent this e ...2 KB (245 words) - 16:07, 15 July 2014
- In these cases we have a mechanism for recording multiple taxon IDs for interacting organisms, but not the relationship between the two org My proposal aims to solve this problem, by allowing annotators to link taxon IDs using a relationship such as host_of or vector_for. Additionally you w ...4 KB (622 words) - 16:30, 9 April 2014
- **DB:Reference, Taxon and GO ID columns are checked for minimal form # inconsistency flag + reason (e.g. taxon constraint violation) ...4 KB (568 words) - 10:14, 14 March 2019
- ...ion to these GAFs happens when they are requested. We need to generate the taxon specific GAFs on a more regular basis. It was agreed on the Ref.genome call ...2 KB (266 words) - 10:55, 12 April 2019
- * <strike>Update on communication mechanisms for changes to the GO taxon file. (Jane)</strike> postphoned until next call ...? Can this be taken care of by inter-ontology links? Not always because of taxon constraints. We all came to an agreement that it is okay to move forward wi ...4 KB (651 words) - 16:33, 9 April 2014
- ! DB Object ID !! DB Object Symbol !! GO ID !! Contributor !! Taxon !! Evidence Code !! PANTHER family !! Reference !! Date ! DB Object ID !! DB Object Symbol !! Qualifier !! GO ID !! Contributor !! Taxon !! Evidence Code !! PANTHER family !! Reference !! Date ...6 KB (797 words) - 11:34, 13 April 2019
- ...n=2.2&rows=10&start=0&fl=*%2Cscore&facet=true&facet.field=type&facet.field=taxon&facet.field=isa_partof_closure_label&fq=&q=*:*&fq=document_category:"bioent facet.field=taxon ...4 KB (597 words) - 15:43, 27 May 2015
- * Update on communication mechanisms for changes to the GO taxon file. (Jane) ====Protein binding and Taxon constraints (Jane)==== ...8 KB (1,211 words) - 16:30, 9 April 2014
- Taxon constraints not filtering errors: ...2 KB (250 words) - 12:22, 29 June 2021
- # Ontology problems that cause bad inferences or taxon violations (eg the heart issue) ...1 KB (209 words) - 14:18, 11 June 2020
- ...software worked fine but the problem was due to the incompleteness of the taxon constraints. ...4 KB (702 words) - 18:53, 23 May 2014
- ***[[Taxon-GO_Implementation_April_2008_onwards#5th_June|Taxon links]] (Jen, Chris) ...3 KB (430 words) - 07:07, 2 April 2009
- * ncbi taxon hierarchy ...1 KB (133 words) - 18:01, 14 July 2014
- ...o and Reactome with the annotations from these groups that have failed the taxon constraint sanity checks. ...2 KB (244 words) - 12:23, 6 May 2014
- * Interacting taxon as an extension rather than as its own file? ...2 KB (286 words) - 12:17, 13 December 2023
- We all need to switch to 2.3.1 before we can include taxon rules in editors file. I've tested it [Paola] and it looks ok. Download fro We're all now switched over to 2.3.1 - Chris will add the taxon constraints to the editors file tomorrow or early next week. ...11 KB (1,667 words) - 15:53, 7 April 2014
- ...ion QC - work continuing; see [[Taxon-GO_Implementation_April_2008_onwards|taxon links]] (Jen, Chris) ...4 KB (451 words) - 07:11, 2 April 2009
- ...mmers; previously reported as [[Taxon-GO_Implementation_April_2008_onwards|taxon links]] (Jen, Chris) ...3 KB (421 words) - 07:11, 2 April 2009
- ...here is a known problem wherein a dog protein is shown with an influenza A taxon id. ...2 KB (218 words) - 15:44, 10 July 2014
- ****Taxon prefix, i.e. 6239 or taxon:6239? ...4 KB (605 words) - 16:44, 10 October 2016
- * How is dual taxon going? ...2 KB (253 words) - 13:53, 4 November 2008
- ...y FB:FBrf0108645|PMID:10231363 IPI FB:FBgn0002562 F gene taxon:7227 20060803 FlyBase ...t growth factor receptor activity PMID:10830168 IPI UniProtKB:P09038 taxon:9606 20091005 MGI ...7 KB (1,157 words) - 11:46, 14 April 2014
- ...nnotation data. The data related to gene products--symbol, name, synonyms, taxon--can be submitted, updated and maintained separately from that concerned wi ...s also no information available about gene product name, synonyms, type or taxon of unannotated gene products in the gp2protein file or in the GAF files. ...25 KB (3,406 words) - 03:34, 13 September 2023
- * Causes taxon constraints problems, see https://github.com/geneontology/go-ontology/issue ...2 KB (280 words) - 12:03, 10 July 2023
- ...taxon constraint. If it has, the source file needs to be modified and the taxon constraint imports need to be regenerated. See: [[Adding_Taxon_Restrictions ...8 KB (1,369 words) - 02:17, 20 April 2022
- * Jen: May Waclaw have access to the internal wiki to help with the taxon-go proposal? Action: Jen to email taxon proposal draft to Waclaw. ...7 KB (1,089 words) - 12:32, 30 June 2014
- ...le of a desirable annotation transformation would be in response to the GO taxon rule that states a gene product can only be annotated to the term 'nucleus' If a viral gene product has been annotated to nucleus from a taxon-independent annotation method - such as InterPro2GO, we would like to trans ...5 KB (815 words) - 06:48, 12 April 2019
- #** Taxon(s) or taxonomic range (it is possible to select for example NBCITaxon:2 for ...2 KB (286 words) - 05:51, 15 March 2024
- * (Pascale) Rules, especially taxon checks: can we have this for the July release? https://github.com/geneontol ...2 KB (251 words) - 11:05, 6 June 2018
- ...an be filtered because the 'with' column will contain a entry from another taxon. ...2 KB (322 words) - 18:58, 23 April 2014
- LAST TIME: Tentatively agreed that disjoints should and taxon constraints should go into main file, with the exception of GCI disjoints Note that reasoning with taxon constraints won't work without expansion. ...9 KB (1,374 words) - 16:06, 1 July 2014
- ==Taxon links== ...d union terms into account. The results are checked into scratch in the go-taxon folder. ...7 KB (1,231 words) - 11:06, 8 April 2014
- *[https://github.com/geneontology/minerva/issues/388 Taxon ID without label #388] ...2 KB (201 words) - 03:21, 26 January 2022
- * How is dual taxon going? ...2 KB (274 words) - 14:46, 18 November 2008
- * ncbi taxon hierarchy ...1 KB (175 words) - 18:01, 14 July 2014
- * GO - taxon links * taxon ...4 KB (620 words) - 18:02, 14 July 2014
- 5. GOA generate gpa/gpi (maybe gaf if you ask nicely) for 142 taxon for all annotations which are passed though step 3 (to be implemented) 6. GO using 142 taxon file for all their pipelines needs, no need to run their own set of checks, ...4 KB (673 words) - 12:03, 11 March 2020
- ...onomic restrictions derived from PAINT could be fed back into the ontology taxon restrictions file [Paul and Jane]. Manager: Jane. ...2 KB (249 words) - 11:19, 16 January 2018
- *Taxon triggers for annotation quality control **[[Taxon-GO_Implementation_April_2009_onwards|Meeting notes]] ...5 KB (599 words) - 10:07, 15 September 2009
- Taxon constraints not filtering errors: ...2 KB (303 words) - 14:51, 30 June 2021